Tomo-tools training - Part 6: editing meta-data

Sometimes, the data comes with wrong parameters/metadata (energy, pixel size), for example by user mistake.

In the previous system, fixing that was as simple as editing the .info text file.

With HDF5, things are less simple because the file cannot be edited in a simple way.

In this part, we see how to edit some metadata, in a hopefully simple way.

Editing metadata with nabu

In the nabu configuration file, the section [dataset] has a overwrite_metadata field.

The following metadata can be changed:

• Pixel size (NB: accounting for magnification)
• sample-detector distance
• Energy

The units must be provided alongside the values.

Examples

The values are separated by a semicolon ;

Example 1

[dataset]
...
overwrite_metadata = energy = 19 kev; pixel_size = 1.6 um

Example 2

[dataset]
...
overwrite_metadata = energy = 80 KeV ; pixel_size = 0.5 um ; distance = 1 meter

Example 3

[dataset]
...
overwrite_metadata = pixel_size = 125 nanometer ; distance = 2 m