reading QString from HDF5

Question

I have a hdf5 file containing some numbers in an attribute like this:

1.0:2.0,2.0:3.0,3.0:4.0

(More precisely the exact attribute:

ATTRIBUTE "azangles" {
            DATATYPE  H5T_STRING {
               STRSIZE H5T_VARIABLE;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
            DATASPACE  SCALAR
            DATA {
            (0): "81.1615:82.76,82.2382:83.8202,83.2983:84.9133,84.375:86.0175,85.4736:87.1545,86.5997:88.2697,87.7258:89.4012,88.83:90.5164,89.989:91.5985,91.0602:92.6752,92.1533:93.7408,93.2025:94.8175,94.2957:95.8777,95.3448:96.9653,96.427:98.053,97.5146:99.1901,98.6298:100.289,99.7504:101.404,100.849:102.53,101.981:103.629,103.079:104.711,104.178:105.782,105.266:106.88,106.337:107.974,107.441:109.072,108.528:110.193,109.644:111.313,110.753:112.467,111.901:113.577,113.033:114.686,114.142:115.79,115.269:116.878,116.34:117.944,117.427:119.004,118.471:120.097,119.564:121.179,120.641:122.294,121.75:123.371,122.838:124.519,123.959:125.623,125.09:126.738,126.183:127.82,127.299:128.908,128.375:129.996,129.457:131.05,130.523:132.144,131.6:133.248,132.709:134.352,133.808:135.467,134.923:136.588,136.033:137.703,137.164:138.801,138.263:139.894,139.356:140.96,140.444:142.042,141.509:143.091,142.581:144.168,143.63:145.261,144.728:146.354,145.811:147.491,146.937:148.568,148.046:149.711,149.161:150.793,150.266:151.886,151.353:152.952,152.446:154.028,153.495:155.11,154.589:156.171,155.649:157.264,156.731:158.373,157.83:159.505,158.95:160.609,160.065:161.724,161.18:162.823,162.285:163.905,163.361:164.938,164.432:165.948,165.454:166.992,166.476:168.014,167.531:169.036,168.53:170.096,169.579:171.129,170.623:172.205,171.672:173.243,172.744:174.287,173.76:175.342,174.825:176.369,175.864:177.413,176.907:178.407,177.913:179.451,178.929:180.478,179.984:181.538,181.016:182.631,182.098:183.702,183.17:184.801,184.268:185.861,185.356:186.949,186.422:187.987,187.487:189.047,188.52:190.069,189.575:191.096,190.585:192.14,191.64:193.2,192.689:194.277,193.749:195.342,194.821:196.397,195.881:197.485,196.952:198.523,198.018:199.572,199.061:200.605,200.11:201.616,201.11:202.643,202.143:203.632,203.143:204.675,204.159:205.714,205.208:206.796,206.246:207.861,207.339:208.927,208.394:210.02,209.487:211.042,210.531:212.102,211.586:213.102,212.624:214.124,213.607:215.129,214.634:216.14,215.634:217.183,216.672:218.216,217.7:219.298,218.771:220.364,219.842:221.413,220.897:222.462,221.94:223.511,223.006:224.55,224.033:225.549,225.06:226.555,226.055:227.609,227.098:228.615,228.115:229.669,229.147:230.729,230.219:231.812,231.273:232.888,232.361:233.937,233.421:235.009,234.481:236.025,235.525:237.052,236.547:238.052,237.568:239.068,238.568:240.101,239.601:241.122,240.617:242.199,241.677:243.248,242.743:244.325,243.787:245.413,244.885:246.462,245.934:247.495,246.984:248.522,248.022:249.549,249.044:250.543,250.06:251.554,251.054:252.587,252.076:253.619,253.098:254.658,254.141:255.701,255.19:256.778,256.245:257.855,257.327:258.898,258.387:259.942,259.426:260.953,260.458:261.996,261.48:263.024,262.524:264.045,263.546:265.1,264.6:266.144,265.627:267.242,266.699:268.297,267.781:269.379,268.841:270.456,269.94:271.489,270.983:272.527,272.021:273.543,273.038:274.565,274.065:275.548,275.059:276.575,276.07:277.614,277.108:278.646,278.124:279.712,279.185:280.767,280.25:281.816,281.299:282.87,282.349:283.909,283.403:284.936,284.431:285.941,285.441:286.968,286.458:288.018,287.507:289.067,288.534:290.127,289.6:291.182,290.66:292.291,291.747:293.346,292.83:294.412,293.884:295.466,294.955:296.488,295.988:297.515,297.015:298.499,298.015:299.515,299.02:300.531,300.048:301.575,301.053:302.624,302.113:303.668,303.14:304.75,304.222:305.81,305.294:306.865,306.354:307.903,307.408:308.941,308.43:309.952,309.463:310.963,310.479:311.995,311.484:313.05,312.534:314.105,313.594:315.17,314.648:316.225,315.703:317.313,316.78:318.356,317.845:319.4,318.889:320.444,319.938:321.454,320.944:322.487,321.976:323.481,322.998:324.52,324.003:325.541,325.047:326.602,326.074:327.673,327.156:328.722,328.195:329.804,329.271:330.842,330.337:331.913,331.386:332.935,332.435:333.968,333.457:334.995,334.49:336.011,335.5:337.066,336.544:338.104,337.593:339.192,338.659:340.263,339.736:341.334,340.807:342.411,341.884:343.46,342.944:344.504,343.993:345.542,345.042:346.564,346.053:347.602,347.091:348.629,348.118:349.706,349.173:350.75,350.239:351.854,351.304:352.936,352.414:353.985,353.463:355.051,354.529:356.078,355.583:357.116,356.605:358.116,357.638:359.138,358.632:0.170288,359.67:1.18652,0.686646:2.25769,1.73584:3.31238,2.79602:4.40002,3.87817:5.4657,4.95483:6.53687,6.01501:7.58057,7.0697:8.61877,8.10242:9.65149,9.14612:10.6732,10.1788:11.7004,11.2006:12.7496,12.2443:13.7988,13.277:14.87,14.3427:15.9027,15.3864:16.9958,16.452:18.0615,17.5452:19.0887,18.5834:20.116,19.6106:21.1212,20.6268:22.1265,21.6321:23.1207,22.6483:24.1315,23.6316:25.1642,24.6643:26.1914,25.686:27.2626,26.7407:28.3008,27.7899:29.3829,28.8501:30.4376,29.9487:31.4868,30.965:32.525,32.0251:33.5248,33.0304:34.563,34.0576:35.5737,35.0739:36.6229,36.1176:37.6721,37.1558:38.7488,38.2104:39.8474,39.3146:40.8966,40.3912:41.9568,41.4349:43.0115,42.5006:44.0332,43.5333:45.0494,44.5551:46.0437,45.5493:47.0654,46.5656:48.0542,47.5763:49.0759,48.5651:50.1251,49.6143:51.1578,50.6525:52.229,51.7072:53.2837,52.7673:54.3384,53.822:55.3986,54.9042:56.4203,55.9149:57.4475,56.9476:58.4363,57.9529:59.491,58.9691:60.5182,60.0183:61.5894,61.062:62.6715,62.1552:63.7482,63.2098:64.8358,64.314:65.907,65.3961:66.9781,66.4563:68.0109,67.511:69.0436,68.5437:70.0488,69.5654:71.0431,70.5542:72.0648,71.5594:73.0865,72.5812:74.1357,73.6194:75.174,74.6686:76.2067,75.6958:77.2833,76.756:78.3215,77.8162:79.3652,78.8489:80.3925,79.8926:81.4197,80.9088:82.4634,81.958:83.4741,82.9688:84.5233,83.996:85.589,85.0671:86.6766,86.1328:87.7588,87.2314:88.8354,88.2971:89.9396,89.4067:90.9668,90.4724:92.0105,91.4996:93.0157,92.5323:94.0375,93.5376:95.0262,94.5428:96.026,95.5261:97.0367,96.5479:98.064,97.5696:99.1351,98.6023:100.184,99.6735:101.217,100.712:102.294,101.766:103.343,102.832:104.365,103.87:105.403"
            }
         }

)

so there is always a start number separated from an end number with :

The datatype is H5T_STRING.

I want to read the Strings, separate them at the : and then convert them to double. I tried this by using QString this way:

QString data[];
double start[];
double end[];

DataAttribute->read(*Datatype, &data);

for (i=0 ; i<LengthData ; i++) {

    QStringList parts = data[i].split(":");

    QString startstr = parts.first();
    QString Stopstr = parts.last();

    start[i]=startstr.toDouble();
    end[i]=Stopstr.toDouble();

}

But it seams that I don't read anything into my data - QString So is it possible to read QString from HDF5?

Or do you have another idea how I can manage this?

EDIT:

I found an example in C but I can't fix the problem in C++

Can someone tell my what the C++ expression for:

H5Tget_size(type)

is? With type an an H5::DataType of an H5 Attribute

Thanks!

EDIT2:

Trying to run the example from Timothy Brown:

I can step through the code BUT there is nothing read in in my string called r. I use std::string r and StrType str_type(PredType::C_S1, H5T_VARIABLE); Result is:

Name : r
    Details:""
    Default:""
    Decimal:""
    Hex:""
    Binary:""
    Octal:""

Answer 1

I am unfamiliar with QString (and C++ for that matter!). However this could be one way that you can tackle it.

Lets create a program to write the test attribute in a file called string.h5. Note that you can use either H5std_string or std::string.

#include <iostream>
#include <string>
#ifndef H5_NO_NAMESPACE
#ifndef H5_NO_STD
using std::cout;
using std::endl;
#endif // H5_NO_STD
#endif
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif

const H5std_string FILE_NAME ("string.h5");
const H5std_string ATT_NAME("test");

int main (void)
{

        H5std_string test("1.0:2.0,2.0:3.0,3.0:4.0");
        /* std::string test = "1.0:2.0,2.0:3.0,3.0:4.0"; */

        H5File *file = new H5File(FILE_NAME, H5F_ACC_TRUNC);

        DataSpace att_space(H5S_SCALAR);
        StrType str_type(PredType::C_S1, H5T_VARIABLE);
        Attribute *att = new Attribute(file->createAttribute(ATT_NAME,
                                str_type, att_space));
        att->write(str_type, test);

        att->close();
        delete att;
        file->close();
        delete file;

        return 0;

}

Compile and run the program:

$h5c++ -o att_w att_w.cpp && ./att_w

Look at the file to check that the attribute is there:

$ h5dump string.h5
HDF5 "string.h5" {
GROUP "/" {
   ATTRIBUTE "test" {
      DATATYPE  H5T_STRING {
         STRSIZE H5T_VARIABLE;
         STRPAD H5T_STR_NULLTERM;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SCALAR
      DATA {
      (0): "1.0:2.0,2.0:3.0,3.0:4.0"
      }
   }
}
}

Now lets try and read the string attribute in and parse it into the start and end vectors.

#include <iostream>
#include <string>
#include <vector>
#ifndef H5_NO_NAMESPACE
#ifndef H5_NO_STD
using std::cout;
using std::endl;
#endif // H5_NO_STD
#endif
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif

const H5std_string FILE_NAME ("string.h5");
const H5std_string ATT_NAME("test");

int main (void)
{

    size_t pos = 0;
    size_t sz  = 0;
    std::string r;
    std::string delimiter = ",";
    std::string token;
    std::vector<double> start;
    std::vector<double> end;
    std::vector<double>::iterator it;

    H5File    *file = new H5File(FILE_NAME, H5F_ACC_RDONLY);
    Attribute *att  = new Attribute(file->openAttribute(ATT_NAME));

    StrType str_type(PredType::C_S1, H5T_VARIABLE);

    att->read(str_type, r);
    /* cout << r << endl; */

    while ((pos = r.find(delimiter)) != std::string::npos) {
        token = r.substr(0, pos);
        start.push_back(std::stod(token, &sz));
        end.push_back(std::stod(token.substr(sz+1)));
        r.erase(0, pos + delimiter.length());
    }
    start.push_back(std::stod(r, &sz));
    end.push_back(std::stod(r.substr(sz+1)));

    att->close();
    delete att;
    file->close();
    delete file;

    return 0;

}

Hope this helps you out.