Basic Usage

Opening an HDF5 File

With hdf5view you can either:

1. Open any HDF5 file with two clicks using the context menu. To enable this, please follow the guide to Setting up the context menu.

or

2. Open the hdf5view application and use the File > Open menu to open a file or drag and drop a file onto the application window. To start the hdf5view application, double click hdf5view.exe in the Scripts folder of your Python distribution.

   Tip

   You can create a desktop link to hdf5view.exe in the Scripts folder of your Python distribution for convenience. A Windows icon file hdf5view.ico is provided in the folder hdf5view/resources/images.

   Note

   If you prefer working at the terminal, you can start the hdf5view application using

   hdf5view
   

   or you can open a file directly using

   hdf5view -f <path/to/my/hdf5file>
   

Initial State of the Application

Once you have opened an HDF5 file with hdf5view, the application window will look like this:

The application window contains five separate widgets:

File Structure Table

The File Structure table (left hand side of the application), shows the structure of the open HDF5 file as a directory tree. By default it is initally at the root group and you can double-click on the folder or click the arrow to expand the tree and navigate to other groups or datasets.

The File Structure table with expanded directory structure and the dataset “3columns” selected.

Central Tabbed Area

The central tabbed area shows the data in a particular dataset. By default a Table tab is visible. You can add Image and Plot tabs here later.

Part of the central tabbed area showing the default Table tab. The filename is shown at the top of the tab.

Attributes Table

The Attributes table (right hand side, top), shows details of any attributes of the selected dataset.

The Attributes table.

Dataset Table

The Dataset table (right hand side, middle), shows details of the type and shape of the data at the selected dataset.

The Dataset table.

Slice Table

The Slice table (right hand side, bottom), shows which slice of the data is currently displayed. There are default slice values for particular dataset types and shapes in hdf5view, which are intended as a sensible starting point. You can change the slice to get a different view of the data.

The Slice table, showing the default slice for the Table tab at a 2D dataset (all rows and columns are shown in the Table).

Detailed guides to using tabs in hdf5view are available in the Table Tab Tutorial, Plot Tab Tutorial and Image Tab Tutorial.

Setting up the context menu

A particularly useful way to use hdf5view is to add an entry to the context menu. That way, you can right-click on any HDF5 file and left-click “Open with hdf5view” from the menu that appears.

On Windows, to get “Open with hdf5view” on the right click context menu, we need to modify the registry. To do this, please follow these 7 steps:

1. Run the registry editor (regedit) as an administrator

2. Navigate to Computer\HKEY_CLASSES_ROOT\*\shell

3. Right-click on shell and select New > Key

4. Name the new key Open with hdf5view

5. Right-click on Open with hdf5view and select New > Key

6. Name the new key command

   The directory structure should now look like this:

   -- Computer
       |-- HKEY_CLASSES_ROOT
         |-- *
            |-- shell
               |-- Open with hdf5view
                  |-- command
   

7. Click on command to select it. In the right-hand window, you should see a table with 3 columns (Name, Type and Data). Right-click on the first entry under the Name column and select Modify. Now find the box value data: and enter the path to hdf5view.exe in the Scripts folder of your Python distribution followed by -f "%1". This should look something like this:

   C:\Program Files\PythonXXX\Scripts\hdf5view.exe -f "%1"
   

   (replace XXX with the number of your Python version e.g. 312 for Python312). Finally select OK.

   Tip

   Enclosing %1 in quotes (as above) "%1" ensures that filenames including spaces are passed correctly to hdf5view.

   Tip

   If you want to add the icon to the context menu as well, right click on the key Open with hdf5view and select New > String Value. In the right-hand window, right-click on the entry in the Name column and select Modify. Set the value name: to Icon. Finally set the value data: to the path to the hdf5view icon as a string, e.g.:

   "C:\Program Files\PythonXXX\Lib\site-packages\hdf5view\resources\images\hdf5view.ico"

Now you can right-click on any HDF5 file and open it with hdf5view.