%% Setup.
cd /Users/jeff/Documents/MATLAB


%% Example -- Read some data

filename = fullfile('hdf5','dHDF5_test.h5');
file = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
dataset = H5D.open(file, '/images/plane interlace');

data = H5D.read(dataset, 'H5ML_DEFAULT', 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT');

imshow(permute(data, [2 1 3]))

% Close the dataset and the file.
H5D.close(dataset);
H5F.close(file);


%% Example -- The example from Tuesday.

dset_data = reshape(int32(1:24), [6 4]);

file_id = H5F.create('dset.h5', 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');

dims = [4 6];
dataspace_id = H5S.create_simple(2, dims, []);

dataset_id = H5D.create(file_id, '/dset', 'H5T_STD_I32BE', dataspace_id, ...
    'H5P_DEFAULT');

H5D.write(dataset_id, 'H5T_NATIVE_INT', 'H5S_ALL', 'H5S_ALL', ...
    'H5P_DEFAULT', dset_data);

H5S.close(dataspace_id);
H5D.close(dataset_id);
H5F.close(file_id);


%% Example -- Hyperslab selection.

% Open a file and get handles to the dataset and dataspace.
file = H5F.open('london_2.h5', 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
dataset = H5D.open(file, '/image');
dataspace = H5D.get_space(dataset);

% How big is the data in the file?
[ndims, dims] = H5S.get_simple_extent_dims(dataspace);

% Let's subset...
offset = [0 0 0];
counts = dims;
dimStride = [];

%offset = [0 1500 1000];
%counts = [3 500 500];
%dimStride = [];

%offset = [0 0 0];
%stride = 4;
%counts = floor([3, (dims(2) - offset(2))/stride, (dims(3) - offset(3))/stride]);
%dimStride = [1 stride stride];

% Read the data.
H5S.select_hyperslab(dataspace, 'H5S_SELECT_SET', offset, dimStride, counts, []);
memspace = H5S.create_simple(3, counts, []);
X_subset = H5D.read(dataset, 'H5T_NATIVE_UINT8', memspace, dataspace, 'H5P_DEFAULT');

% Show the data.
imtool(X_subset)

% Clean up.
H5S.close(dataspace);
H5S.close(memspace);
H5D.close(dataset);
H5F.close(file);


%% Example -- Handle Errors.  One way...

filename = fullfile('hdf5', 'dHDF5_test.h5');

file = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');

try
    H5D.open(file, '/images/GuessWhat_TheImageIsNotHere');
catch
    disp('Oops!  Something went wrong.')
end

lasterror


%% Another way to handle errors...

% Since there is no dogpile dataset, we will walk the error stack
H5E.walk('H5E_WALK_UPWARD', @errorIterator)

% Close the dataset and the file.
H5F.close(file);

% Clear the error stack
H5E.clear

% Since the stack has been cleared, we will not enter the error iterator
H5E.walk('H5E_WALK_UPWARD', @errorIterator)


%% Example -- Query attributes.
file = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
dataset = H5D.open(file, '/images/plane interlace');

numAtts = H5A.get_num_attrs(dataset)

% Open attribute 0 and get name
attr0 = H5A.open_idx(dataset, 0);
attrNames = H5A.get_name(attr0)

% Open attribute 1 and get type
attr1 = H5A.open_idx(dataset, 1);
attrType = H5A.get_type(attr1)
attrClass = H5T.get_class(attrType)
actTypeComparison = H5ML.compare_values(attrClass, 'H5T_STRING')

% Open attribute 2 and get space
attr2 = H5A.open_idx(dataset, 2);
attrSpace = H5A.get_space(attr2);
numPoints = H5S.get_simple_extent_npoints(attrSpace)


%% Look at the contents of an object
get(file)
get(dataset)
get(attrSpace)

% Notice that the objects contain a callback to close the object at
% destruction and a listener to prevent the objects from doing bad things
% when the HDF5 identifiers become stale.


%% Example -- Get the attribute data.
file = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
dataset = H5D.open(file, '/images/plane interlace');

% Open attribute IMAGE_MINMAXRANGE
attr = H5A.open_name(dataset, 'IMAGE_MINMAXRANGE');

% Read from attribute.  Note the use of H5ML_DEFAULT
minMaxRange = H5A.read(attr, 'H5ML_DEFAULT')

% Clean up.
H5A.close(attr);
H5D.close(dataset);
H5F.close(file);

%% Example -- Add an attribute to a dataset.

filename  = 'MyNewFile.h5';
file = H5F.create(filename, 'H5F_ACC_TRUNC', ...
                  'H5P_DEFAULT', 'H5P_DEFAULT');

% Create a group and dataset
group = H5G.create(file, '/Data', 0);

rank = 1;
dims = 7;
dataspace = H5S.create_simple(rank, dims, []);
dataset = H5D.create(file, '/Data/Fibonacci', 'H5T_STD_I32LE', ...
                     dataspace, 'H5P_DEFAULT');  

H5D.write(dataset, 'H5ML_DEFAULT', 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', ...
          int32([1 1 2 3 5 8 13]));

% Create attribute
rank = 2;
dims = [2, 2];
attrDataspace = H5S.create_simple(rank, dims, []);
attrName = 'CDATA_RANGE';
attr = H5A.create(dataset, attrName, 'H5T_STD_I32LE', ...
                  attrDataspace, 'H5P_DEFAULT');   

% Write attribute
attrData = int32([1, 2; 3, 4]);
H5A.write(attr, 'H5ML_DEFAULT', attrData);

% Close attribute
H5A.close(attr);


%%

% Verify the attribute is present 
H5A.get_num_attrs(dataset)

% Read attribute data
attr2 = H5A.open_idx(dataset, 0);
H5A.get_name(attr2)
H5A.read(attr2, 'H5ML_DEFAULT')

% Delete attribute
H5A.delete(dataset, attrName);

% Verify deletion
H5A.get_num_attrs(dataset)

% Close open identifiers
H5A.close(attr2);
H5S.close(attrDataspace);
H5D.close(dataset);
H5S.close(dataspace);
H5G.close(group);
H5F.close(file);


%% Look at the file with h5dump
!hdf5/h5dump MyNewFile.h5


%% Example - Create a variable-length array.

% Create vlen datatype
datatype = H5T.vlen_create('H5T_STD_I8LE');

% Create dataspace
rank = 2;
dims = [4 1];
dataspace = H5S.create_simple(rank, dims, []);

% Create file and dataset
filename = 'MyVlenFile.h5';
file = H5F.create(filename, 'H5F_ACC_TRUNC', 'H5P_DEFAULT',...
                  'H5P_DEFAULT');
dataset = H5D.create(file, 'dataset1', datatype, dataspace, ...
                     'H5P_DEFAULT');
                 
% Create the VL data 
for i = 1:prod(dims)
    vlData{i} = int8(magic(i+3));
end

% Write the data
H5D.write(dataset, datatype, 'H5S_ALL', 'H5S_ALL',...
          'H5P_DEFAULT', vlData);

% Get size
H5D.vlen_get_buf_size(dataset, datatype, dataspace);
% Expected size: magic(1) - 1 byte, magic(2)- 4 bytes, magic(3) - 9 bytes,
% magic(4) - 16 bytes - Total 30 bytes

% Close open identifiers
H5T.close(datatype);
H5S.close(dataspace);
H5D.close(dataset);
H5F.close(file);


%% Look at the file with h5dump
!hdf5/h5dump MyVlenFile.h5


%% Example -- Use an iterator.
filename = fullfile('hdf5', 'dHDF5_test.h5');

file = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
dataset = H5D.open(file, '/images/plane interlace');

% Call the same function on each attribute in the dataset.
% (See attributeIterator.m)
H5A.iterate(dataset, 0, @attributeIterator);

% Close the dataset and the file.
H5D.close(dataset);
H5F.close(file);


%% More examples -- References
addpath /Users/jeff/Documents/MATLAB/hdf5/

%h5_ref2reg