Hello all. I'm new to the HDF5 world, so I seek the wisdom of the elders.
I am trying to write a tool that will scan through an HDF file and pull out
basic information (group and dataset names, data names, data values (if
string), etc.). I decided to write it in C#, since I am the most familiar
with that, and since I hoped to one day wrap this tool into a set of tools
that will all be accessed in one windows application. I downloaded and
installed the HDF5DotNet package, and in a few hours was up and running,
getting dataset names and gorup names and value names.
My problem is trying to read in strings. I came across this group through a
Google search on my issue, and found a recent thread by Scott Mitchell (
that described his issues with reading strings with HDF5DotNet, but neither
my own attempts to solve this problem, nor the solutions provided to him
have been 100% effective.
Firstly, my initial stab at trying to read a string (in this case, an
char  data = new char [H5T.getSize(dataType)];
H5A.read(attributeId, dataType, new H5Array<char>(data));
Console.WriteLine(" - Value: "+new string(data));
This is probably wrong, but I did notice that while the output was mostly
garbage, the LAST character would print out fine. The output would look
- Value: ??E
when it was supposed to output "IMAGE". Or whatever.
So, I tried the solution proposed to Scott Mitchell, and used the code from
the example HDF5DotNet project linked to him, plus his comments after he
says he solved his problem. For the sample HDF5 'strings.h5', the solution
worked great. I was able to output string values left and right. However,
if I tried to modify the strings.h5 to add fixed length string attirbutes,
the values of the attributes would print out blank. And when I tried to
open other sample HDF5 files (hdf5_test.h5, and a few of the files I will
eventually be scanning), the values output were either blank or garbage.
Help! What am I doing wrong? The datatype I am passing to the read
function I am getting off of H5T.getType() against the dataset/attribute I
am trying to read. Do I need to modify this somehow? What am I missing?
For completeness sake, here's the code I am trying from Scott Mitchell's
from inside my attributes iterate function:
if (H5T.getClass(dataType) == H5T.H5TClass.STRING)
Chararray data = new Chararray;
H5A.read(attributeId, dataType, new
Console.WriteLine(" - Value: " +
//this defines the struct used to read in the string data
//since it is unsafe we need to use the layout to define the struct
public unsafe struct Chararray
private double* recordedText;
//an initializer to get and set the char* since it is unsafe
public double* RecordedText
recordedText = value;
public override string ToString()
string s = "";
//the HDF5 STRING is not a string but in fact a char *
//since it is we need to translate the return into a pointer
IntPtr ipp = (IntPtr)this.recordedText;
//This call is used to transform the pointer into the value
of the pointer.
//NOTE: this only works with null-terminated strings.