Set correct sample tilt for TKD dataset read from Bruker HDF5

[hakonanes]

An on-axis TKD dataset read from a Bruker HDF5 file may have a sample tilt σ = 0 degrees and a detector tilt θ of, say, 5.8 degrees. In kikuchipy's detector-sample geometry, this case corresponds to the detector looking at the sample almost edge-on. This is obviously incorrect for on-axis TKD.

The correct in this case is σ' = σ + 90. But what are the rules for when to do this?

In a file with these tilts (generously provided by Alice Bastos da Silva Fanta from DTU), the following image of the Bruker Esprit 2.x coordinate systems is included in the EBSD.original_metadata.Coordinate_Systems.ESPRIT_Coordinates:

The original metadata also contains a "coordinate system ID" equal to 5 in this case. My assumption is that this value signifies that we can add 90 degrees to σ, but I don't know as I don't have access to a Bruker Esprit manual. @IMBalENce, @Fred-Ad, do you know what this ID means? Or know someone who has access to a Bruker Esprit 2.x manual?

I'm inclined to add 90 degrees to the sample tilt of the detector returned with the signal if we can verify that the coordinate system ID is equal to 5.

[hakonanes]

Re-reading the excellent supplementary material to the tutorial paper by Britton et al. (2016) https://doi.org/10.1016/j.matchar.2016.04.008, the tilt of the sample relative to the detector is given by τ = τ_sample - 90 - θ. In this case, this would be τ = 0 - 90 - 5.8 = -95.8, which is incorrect.

[hakonanes]

@lukmuk, from hyperspy/rosettasciio#103 I understand that you're a Bruker user. Do you know what a Coordinate System ID of 5 signifies? I'm trying to figure out how I can know that data is acquired with an on-axis TKD detector-sample geometry.

[IMBalENce]

@hakonanes I have checked all my Bruker user manuals and could not find any information on this Coordinate System ID. I'll send you the latest version I have in email. I will keep searching in case of any clues.

[hakonanes]

Thanks @IMBalENce, I'll have a look at the manuals as well.

[lukmuk]

@lukmuk, from hyperspy/rosettasciio#103 I understand that you're a Bruker user. Do you know what a Coordinate System ID of 5 signifies? I'm trying to figure out how I can know that data is acquired with an on-axis TKD detector-sample geometry.

Hello @hakonanes ! Yes, we have a Bruker system and I am starting to get into EBSD in the last few months. Kikuchipy helps a lot in processing and understanding the concepts! 😅

Regarding the question:

• I could not find much info in the manual (I have Esprit 2.1 and 2.3, but not much info on this problem here).

• Esprit has a "TKD mode" option in the PC calibration, which I thought may add the additional 90° rotation and may add the system ID (?). However, according to my manual, this "TKD mode" checkbox is only required for the configuration with "flat" TEM sample and "normal"/vertical EBSD detector position (i.e., not on-axis TKD). So I guess this will not set the system ID (but may be double-checked by others?).
  

• The system ID may be set by the settings in the online version for Esprit on the SEM, where the admin/user has to set if the normal off-axis EBSD or on-axis TKD detector is currently mounted. This may set the required additional 90° detector tilt. I will check for info when I am on the microscope next time. Maybe there is some info.

Unfortunately, we do not have the option to export to Bruker's hdf5 format from our Bruker Esprit software, so I cannot check possible changes to the hdf5 metadata. Maybe someone else has access to TKD + Bruker-hdf5-export option?