HDF5 Data File Tree Structure : h5tree

Print the tree structure of any HDF5 file.

Note

The tree subcommand replaces the now-legacy structure subcommand and also replaces the h5toText program from the spec2nexus project.

How to use h5tree

Print the HDF5 tree of a file:

$ punx tree  path/to/file/hdf5/file.hdf5

the help message:

 1  [linux,512]$ punx tree -h
 2  usage: punx tree [-h] [-a] [-m MAX_ARRAY_ITEMS] infile
 3
 4  positional arguments:
 5    infile                HDF5 or NXDL file name
 6
 7  optional arguments:
 8    -h, --help            show this help message and exit
 9    -a                    Do not print attributes of HDF5 file structure
10    -m MAX_ARRAY_ITEMS, --max_array_items MAX_ARRAY_ITEMS
11                          maximum number of array items to be shown

Example

Here’s an example tree view of a NeXus HDF5 data file (writer_1_3.h5 from the NeXus documentation 1):

 1  [linux,512]$ punx tree data/writer_1_3.hdf5
 2  data/writer_1_3.hdf5 : NeXus data file
 3    Scan:NXentry
 4      @NX_class = NXentry
 5      data:NXdata
 6        @NX_class = NXdata
 7        @signal = counts
 8        @axes = two_theta
 9        @two_theta_indices = [0]
10        counts:NX_INT32[31] = [1037, 1318, 1704, '...', 1321]
11          @units = counts
12        two_theta:NX_FLOAT64[31] = [17.926079999999999, 17.925909999999998, 17.925750000000001, '...', 17.92108]
13          @units = degrees
1

writer_1_3 from NeXus: http://download.nexusformat.org/doc/html/examples/h5py/writer_1_3.html

source code documentation

Describe the tree structure of any HDF5 file

Hdf5TreeView(filename)

Describe the tree structure of any HDF5 file
class punx.h5tree.Hdf5TreeView(filename)[source]

Describe the tree structure of any HDF5 file

Example usage showing default display:

mc = Hdf5TreeView(filename)
mc.array_items_shown = 5
show_attributes = False
txt = mc.report(show_attributes)
report(show_attributes=True)[source]

Return the structure of the HDF5 file in a list of strings.

The work of parsing the datafile is done in this method.

The hierarchy of the file is represented by indentation using spaces. Attributes are signified using @. Group/dataset names are separated from their datatypes using :. A preview of the value of an item follows the =. For example:

1 [
2     '/tmp/tmpb7iqqapu.hdf5',
3     '  external_data:NXdata',
4     '    @NX_class = NXdata',
5     '    @signal = x',
6     '    x:int64 = 0',
7 ]