%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Disclaimer: this info is provided as is and is not part of the IceRadar application. It is provided to help users to
%take advantage of the hdf5 file open format, which is the file format used in IceRadar. For more information
%about IceRadar, contact Blue System Integration Ltd , Vancouver BC. Canada. http://www.bluesystem.ca ; info@bluesystem.ca .
%If modifications and improvements on how to work with IceRadar files with Matlab are made, we would welcome sharing this information.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Return file info
fileinfo = hdf5info('glacier2_UTM_may08.h5 ');
%it returns:
%fileinfo = 
%
%          Filename: 'glacier2_UTM_may08.h5 '
%       LibVersion: '1.6.2'
%           Offset: 0
%         FileSize: 54318792
%   GroupHierarchy: [1x1 struct]

% return hierarchy
toplevel = fileinfo.GroupHierarchy;
%it returns: 
%toplevel = 
%
%      Filename: 'glacier2_UTM_may08.h5 '
%          Name: '/'
%        Groups: [1x12 struct]
%      Datasets: []
%     Datatypes: []
%         Links: []
%    Attributes: []

% one can see the Groups have 12 elts: these are the 12 "Lines" in the
% file. Datasets and so on are nested inside these groups, which may be
% why they do not appear for now.

%let' s look at the structure Groups in the object Groups
lines = fileinfo.GroupHierarchy.Groups

%lines = 
%
%1x12 struct array with fields:
%    Filename
%    Name
%    Groups
%    Datasets
%    Datatypes
%    Links
%    Attributes

% it returns a structure with amongst other, another set of groups.

%let's look at a particular line's content:
fileinfo.GroupHierarchy.Groups(1).Groups(1)
%the name will appear, in this case: /line_0/location_0

fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1)
% Then the dataset will appeart with the command above as: 
% '/line_0/location_0/datacapture_0'

fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1).Datasets(1)
%will show the dataset name etc... and the existance of attribues
%      Filename: 'glacier2_UTM_may08.h5 '
%          Name: '/line_0/location_0/datacapture_0/echogram_0'
%          Rank: 1
%      Datatype: [1x1 struct]
%          Dims: 200
%       MaxDims: -1
%        Layout: 'chunked'
%    Attributes: [1x4 struct]
%         Links: []
%     Chunksize: []
%     FillValue: 0

fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1).Datasets(1).Attributes(1)
%will show the attribure structure:

%    Filename: 'glacier2_UTM_may08.h5 '
%    Name: [1x58 char]
%    Value: [1x1 hdf5.h5string]


fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1).Datasets(1).Attributes(1).Name
% will returbn the 1st attribure of the dataset's name
% /line_0/location_0/datacapture_0/echogram_0/Save timestamp
% same idea for Attributes 2 to 4: the name can be retrieved.

fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1).Datasets(1).Attributes(2).Value
% this will return the value of the attribure 
%hdf5.h5string:
% 
%       Name: ''
%     Length: 4
%    Padding: 'nullterm'
%       Data: 'Ј'

fileinfo.GroupHierarchy.Groups(1).Groups(1).Groups(1).Datasets(1).Attributes(2).Value.data
%however the data seems to be binary. 

%Remembering arrays in Matlab are indexed starting at 1, while index starts at 0 in LabVIEW:
%the dataset name is defined this way >> datasetname
datasetname = '/line_0/location_0/datacapture_0/echogram_0';
filename = 'E:\Project - Active\5017-01 SFUGlacio - Radar\Software\Data\data_kluane_May08\RadarData_withUTM_withPicking\glacier2_UTM_PICK_may08.h5';
data = hdf5read(filename,datasetname);
plot (data);
%this will plot echogram from this location.

% for the attribures:
attributename = '/line_0/location_0/datacapture_0/echogram_0/GPS Cluster- MetaData_xml'
hdf5read(filename,attributename)
%returns
%hdf5.h5string:
 
%       Name: ''
%     Length: 4
%    Padding: 'nullterm'
%      Data: '0Ý	'

%which is still binary...

%from the HDF5TOOLS librarie found at:
%http://www.mathworks.com/matlabcentral/fileexchange/17172
%the following steps can retrieve the attributes, and hence the GPS info,
%saving time, scope settings.

%we already seen that the following code returns a radargram: 
datasetname = '/line_0/location_0/datacapture_0/echogram_0';
filename = 'E:\Project - Active\5017-01 SFUGlacio - Radar\Software\Data\data_kluane_May08\RadarData_withUTM_withPicking\glacier2_UTM_PICK_may08.h5';
data = hdf5read(filename,datasetname);
plot (data);

%now to return the attributes:
attributename1 = 'Save timestamp'
d=h5attget(filename, datasetname,attributename1)

d = 

    '07/05/2008_11:46:07 AM'  
%Here d is returned as a string.
%for the other attribures: 
attributename2 = 'GPS Cluster- MetaData_xml'

attributename2 =

GPS Cluster- MetaData_xml

d=h5attget(filename, datasetname,attributename2)

d = 

    [1x718 char]
% The Char has to be converted to a string, in our case an xml string
x=char(d) 
%will return the attribute as a string, xml, that can then be parsed using
%xml parsing tools, or some string-based coding. From this GPS data in Lat
%etc.. can be retrieved.

%last thing to retrieve are the actual names of the lines and location.
%these were stored as "comment" of the object. So the HDF5 API function
%"H5Gget_comment" should be called for this. No examples found on this so
%far. See HDF web site for the command:
%http://www.hdfgroup.org/HDF5/doc1.6/RM_H5G.html#Group-GetComment