Renishaw reader calculates the scale for the microscope image incorrectly

[Asharits]

Describe the bug

In the Renishaw reader, the scale for the microscope image (WHTL) is being calculated incorrectly for hyperspectral maps. This causes the mapped area (red box) to show up in the wrong area.

To Reproduce

I verified this by comparing images to mapped area in the WiRE versus what Hyperspy is plotting for multiple datasets.

Expected behavior

I am not sure where in the reader this is being calculated but it is an easy fix. In the original metadata for the microscope image, FocalPlaneXYOrigins contains the origin for X and Y. FocalPlaneXResolution and FocalPlaneYResolution contains the length of the image. These values just need to be added to the origin values and then divided by the image shape to obtain the correct scale.

I tested this out on some of my datasets and it fixed the scale and the red box was now in the correct place.

Python environment:

• RosettaSciIO version: 0.6
• Python version: 3.11.8
• HyperSpy version: 2.1.1

[ericpre]

Are you saying that the offset and scale of the microscope image are incorrect but the hyperspectral maps are correct?

The scale and offset of the microscope image are calculated in

rosettasciio/rsciio/utils/image.py

Lines 42 to 70 in e499110

	def _parse_axes_from_metadata(exif_tags, sizes):
	# return of axes must not be empty, or dimensions are lost
	# if no exif_tags exist, axes are set to a scale of 1 per pixel,
	# unit is set to None, hyperspy will parse it as a traits.api.undefined value
	offsets = [0, 0]
	fields_of_views = [sizes[1], sizes[0]]
	unit = None
	if exif_tags is not None:
	# Fallback to default value when tag not available
	offsets = exif_tags.get("FocalPlaneXYOrigins", offsets)
	# jpg files made with Renishaw have this tag
	fields_of_views = exif_tags.get("FieldOfViewXY", fields_of_views)
	unit = FocalPlaneResolutionUnit_mapping[
	exif_tags.get("FocalPlaneResolutionUnit", unit)
	]
	axes = [
	{
	"name": name,
	"units": unit,
	"size": size,
	"scale": fields_of_views[i] / size,
	"offset": offsets[i],
	"index_in_array": i,
	}
	for i, name, size in zip([1, 0], ["y", "x"], sizes)
	]
	return axes

And what it does seems to be consistent with your description of how it should be calculated.

As I remember, the data that I have doesn't have this issue. Can you share files and screenshots?

[Asharits]

Hmm, I wonder why it isn't working for me. Below is a screenshot of the same dataset from WiRE and in Hyperspy. You can see the map area does not match up.

WiRE Screenshot

Hyperspy Screenshot

[Asharits]

To me it looks like an issue with the way scale is calculated using FieldOfViewXY. Maybe there is a difference depending on the version of WiRE? I am on 5.6