Data Management

4D-Explorer is based on the HDF5 file format. HDF5 files consist of groups and datasets, similar to folders and files in a computer operating system. Groups can contain other groups and datasets, forming a hierarchical structure that facilitates the organization and management of complex data.

Creating a New HDF5 File

To create a new HDF5 file, open the “File” menu at the top left of the main interface and press the New HDF5 File button. This will open a dialog to choose the name and storage path for the new HDF5 file. We will name the new HDF5 file 4D-Explorer-test-dataset.h5. Afterward, a dialog will automatically pop up to select the newly created HDF5 file, which you can then open.

Create a New File

In the newly created HDF5 file, which is empty, there is only one item in the File panel on the left, representing the newly created HDF5 file 4D-Explorer-test-dataset.h5. We will first create a group to place the datasets we are about to import. To create a group, right-click on 4D-Explorer-test-dataset.h5 in the left panel and select New (with a + icon) from the pop-up menu.

Create a New Group 1

Creating a New Group

In the opened Create Item dialog, there are three fields to fill in:

  • Location: This specifies where the group should be created. The default is /, which, for those familiar with Unix/Linux, represents the root directory. In HDF5 files, this means the item is being created at the root level and does not belong to any group. Clicking the Browse... button allows you to browse and select a group to place the new item in. However, since our HDF5 file currently has no groups, we can only select the root directory.

  • Name: This is the name of the new group. The default is untitled, but we will change it to a desired name, such as gold_nanoparticle.

  • Type: Here, we select Group, indicating that we are creating a group rather than a dataset.

Create a New Group 2

If everything goes smoothly, you should see a new item under 4D-Explorer-test-dataset.h5 in the File panel on the left, named gold_nanoparticle_06, with a folder icon. This is the group we just created.

Creating Multiple Groups

We provide three test datasets, so we will create three groups here, named:

  • gold_nanoparticle_06

  • gold_nanoparticle_07

  • MoS2_14

Group Operations

Right-clicking on a group will reveal a menu similar to the one we just saw, with operations that can be performed on a group, including:

  • New: Create a new group or dataset within the group.

  • Import 4D-STEM dataset: Import a 4D-STEM dataset into the group.

  • Move/Copy/Rename/Delete: Edit the group (move, copy, rename, delete).

  • Attributes: View the group’s attributes.

Feel free to add, delete, or modify these groups as needed, but be aware that some operations are irreversible.

Warning

Always be cautious when deleting something.