Fix quant scaling error #2090
Fix quant scaling error #2090
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This change will not change the units in the original spectrum image, just locally within the function for the correct electron dose to be calculated. |
…gnal is not changed when doing a quantification.
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ericpre
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@k8macarthur I have rebased your branch on Rnp to fix some left over of a merge conflict and the merge commits. You will need to checkout this branch. |
hyperspy/_signals/eds_tem.py
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| if self.axes_manager[0].units != 'nm': | ||
| self.axes_manager[0].convert_to_units('nm') | ||
| if self.axes_manager[1].units != 'nm': | ||
| self.axes_manager[1].convert_to_units('nm') |
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This is changing the units in place. The following should work:
pixel_size = []
# in case there are more than 2 navigation axes.
for axis in self.axes_manager.navigation_axes[:2]:
pixel_size.append(axis.convert_to_units('nm', inplace=False)[0])In particularly, for a dataset with navigation dimension > 2, how do we know if we pick the correct navigation axes? Here, I assume that the first two items of the axes_manager.navigation_axes are the "x" and "y" spatial dimension but it could something else!
Depending on how this is implemented, this should be documented.
hyperspy/_signals/eds_tem.py
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| if self.axes_manager[0].units != 'nm': | ||
| self.axes_manager[0].convert_to_units('nm') | ||
| if self.axes_manager[1].units != 'nm': | ||
| self.axes_manager[1].convert_to_units('nm') | ||
| pixel1 = self.axes_manager[0].scale | ||
| pixel2 = self.axes_manager[1].scale |
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By the method to get the dose will be wrong for linescan: self.axes_manager[1].scale could be a signal axis..
| res2 = s2.quantification(intensities, method, factors) | ||
| np.testing.assert_allclose(res[0][0].data, res2[0][0].data) | ||
| # Check that the quantification doesn't change the units of the signal | ||
| assert s.axes_manager[0].units == 'µm' |
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This is this assertion which need to be true. At the moment, the units are changed inplace.
…uant_Scaling_Error-RNP
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I have fixed the comments of my review. |
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LGTM |
Description of the change
The dose calculation function used for cross section quantification previously assumed that the units of the navigation axis are in 'nm'. Therefore I've added a check to the function and convert_to_units for when the units are not 'nm'.
Test to check whether or not different units produces the same quantification results was also added.
As this is a bug fix no update to the user guide is needed.