Detector orientation with euler angles: simulations from master patterns and GeometricalKikuchiPatternSimulation #691
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Hi @tgwoodcock, Thank you for this PR and for the kind words! Glad you use kikuchipy and find it useful :) I don't have time to look at your changes in detail now. From the top comment it seems like they fix a bug and add some nice new features. Although I believe we have to iterate on the additions to the public API (naming of the Euler angles and matrices). I hope to get back to you within a week at the latest so we can get this in. |
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Hi @tgwoodcock, is it OK if I push changes that makes the test suite pass? And have you done any benchmarking of refinement and projection from master pattern to detector after making your changes? |
hakonanes
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Nov 17, 2024
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I hope I have fixed the problems now - the test suite passes on my Windows machine with Python3.12. Have updated my remote branch.
Not with refinement but I did benchmark getting the direction cosines. The performance was slower with the new version. I'll look into whether this can be improved. |
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I assume you want to make the changes I suggested? |
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If you merge in recent changes in develop, tests should pass. |
Added an attribute self.twist, which holds the rotation angle of the detector about the normal to the detector screen (Zd). This defaults to 0 and can be passed during instantiation. Defined a dependent property, self.euler which holds the three detector Euler angles in degrees. These describe the orientation of the detector. self.euler[0] == self.azimuthal self.euler[1] == 90 + self.tilt self.euler[2] == self.twist The methods EBSDDetector.save() and EBSDDetector.load() were updated so that the EBSDDetector.twist attribute is additionally saved. The test method TestSaveLoadDetector.test_save_load_detector() in tests/test_detectors/test_ebsd_detector.py has been updated to include an extra assert statement to check that the saved and read twist angles are the same. All tests in tests/test_detectors/test_ebsd_detector.py pass with the current code. Signed-off-by: tgwoodcock <[email protected]>
This property returns an orix.quaternion.Rotation representing the orientaiton matrix which transforms vectors in the sample coordinate system CSs, to the detector coordinate system, CSd. Signed-off-by: tgwoodcock <[email protected]>
The __repr__ method now prints the detector twist angle as well as the detector tilt and detector azimuthal. The associated test has been updated. All tests in test_ebsd_detector.py are passing. Signed-off-by: tgwoodcock <[email protected]>
Modified the calculation of the orientation matrix u_s_bruker in KikuchiPatternSimulator.on_detector(). Previously u_s_bruker was determined from the 'total_tilt', which only considered EBSDDetector.sample_tilt and EBSDDetector.tilt but NOT EBSDDetector.azimuthal. Now EBSDDetector has the detector Euler angles, which describe the full orientation of the detector and these can be used to calculate u_s_bruker. In this way, the full orientation of the detector can be considered when making simulations to overlay on patterns. This will give a much better fit for cases where the detector azimuthal angle was non-zero (i.e. EBSDDetector.euler[0] != 0) or where the third detector Euler angle was non-zero. Signed-off-by: tgwoodcock <[email protected]>
….util._master_pattern.py The functions _get_direction_cosines_for_fixed_pc() and _get_direction_cosines_for_varying_pc() have been modified. The previous functions used an algorithm adapted from EMSoft to calculate the direction cosines of the detector pixels. This has now been changed and the functions use an orientation matrix approach, adapted from that in the tutorial paper by Britton et al. This enables the detector tilt, azimuthal and twist, i.e. all 3 detector Euler angles, to be correctly incorporated in the pattern simulation. The function _get_direction_cosines_from_detector() has been updated to reflect the new signatures of the other two functions. Signed-off-by: tgwoodcock <[email protected]>
…sociated test The funtion _get_cosine_sine_of_alpha_and_azimuthal() has been removed from src/kikuchipy/signals/util/_master_pattern.py as it is no longer needed. The function import and associated test in tests/test_signals/test_ebsd_master_pattern.py has also been removed. Signed-off-by: tgwoodcock <[email protected]>
…direction_cosines_for_varying_pc() In tests/test_rotation/test_rotation.py: In TestRotationVectorTools.test_rotate_vector(), added the instantiation of an EBSDDetector so that the gnomonic_bounds can be passed into the new signature of _get_direction_cosines_for_fixed_pc(). Modified the arguments in the function call accordingly. In tests/test_signals/test_ebsd_master_pattern.py: In TestProjectFromLambert.test_get_direction_cosines(), updated the arguments in the function call to _get_direction_cosines_for_fixed_pc(). Added a further call to that function but WITHOUT .py_func and added a further assert statement to check that the results with and without .py_func are the same (as recommended in the contributing guidelines). In TestProjectFromLambert.test_get_direction_cosines_for_multiple_pcs(), updated the arguments in the function call to _get_direction_cosines_for_varying_pc(). Added a further call to that function but WITHOUT .py_func and added a further assert statement to check that the results with and without .py_func are the same (as recommended in the contributing guidelines). In TestProjectFromLambert.test_detector_azimuthal() As the function_get_direction_cosines_for_fixed_pc() has been modified, the small rotation in the EBSD pattern simulated from the master pattern for tilt!=0 and azimuthal!=0 is no longer present. The mean values of the data in the simulated patterns sim2 and sim3 in the above test are therefore very slightly different to the old values. The mean values have been updated. The above tests are now all passing. Signed-off-by: tgwoodcock <[email protected]>
These changes are necessary due to the new signature of the functions for getting direction cosines in src/kikuchipy/signals/util/_master_pattern.py. Added a new module src/kikuchipy/_utils/_gnonomic_bounds.py with a function get_gnomonic_bounds(). This is used by the _solvers and _objective_functions to calculate the gnomonic bounds of a detector without needing an EBSDDetector Python object. Added a test class for the new function for getting a single set of gnomonic bounds. In src/kikuchipy/indexing/_refinement/_refinement.py, modified the function _RefinementSetup.set_fixed_parameters() to pass om_detector_to_sample through to the _solvers and _objective_functions, rather than the detector tilt angles, which are no longer needed. The functions _refine_orientation_chunk_scipy() and _refine_orientation_chunk_nlopt() have been similarly updated. In src/kikuchipy/indexing/_refinement/_solvers.py, _refine_orientation_solver_scipy() and _refine_orientation_solver_nlopt() were modified to handle the new way of calculating direction cosines. In src/kikuchipy/indexing/_refinement/_objective_functions.py, _refine_pc_objective_function() and _refine_orientation_pc_objective_function() were modified to handle the new way of calculating direction cosines. Imports to these modules have been added/modified accordingly. Signed-off-by: tgwoodcock <[email protected]>
The above function in the suite TestEBSDRefineOrientationPC has been modified by adding a trust region as an argument in the call to s.refine_orientation_projection_centre() with the method "differential_evolution". This was necessary because the new version of _refine_orientation_pc_objective_function() in indexing\_refinement\_objective_functions.py requires the calculation of gnomonic_bounds. If pc is (0, 0, 0), this cause divide by zero errors in the function get_gnomonic_bounds() in _utils\_gnomonic_bounds.py. Adding the trust region (same parameters as in the earlier call to s.refine_orientation_projection_centre() within the same test function) solves this problem. The test test_refine_orientation_pc_pseudo_symmetry_scipy() now passes, as do ALL the tests in tests/test_indexing/test_ebsd_refinement.py. Signed-off-by: tgwoodcock <[email protected]>
Added the new module kikuchipy/_utils\_detector_coordinates.py. This contains functions for converting coordinates on the detector screen (EBSD pattern) from pixels to gnomonic units. Also added associated tests. Signed-off-by: tgwoodcock <[email protected]>
Added a property coordinate_conversion_factors, and a method convert_detector_coordinates() to the EBSDDetector. These call the functions in kikuchipy/_utils/_detector_coordinates.py The EBSDDetector can now convert between pixel and gnomonic coordinates in both directions. Added appropriate tests for the new functions. Signed-off-by: tgwoodcock <[email protected]>
This class in tests/test_signals/test_ebsd_master_pattern.py helps to test the fit between an EBSD pattern generated from a master pattern and an associated GeometricalKikuchiPatternSimulation for different detector orientations. Signed-off-by: tgwoodcock <[email protected]>
The new EBSDDetector property sample_to_detector returns a Rotation. The test checks the type is correct and that values are correct according to some expected values for different parameters. Signed-off-by: tgwoodcock <[email protected]>
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All tests are passing on my local windows machine. Requested changes have been completed. |
Signed-off-by: tgwoodcock <[email protected]>
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Description of the change
Hi @hakonanes and the kikuchipy team,
firstly, many thanks for kikuchipy - it's a great library which we use a lot in our work!
The focus of this PR is to include the detector Euler angles as a means of describing the full orientation of the detector and to use these in simulating EBSD patterns from master patterns and in producing lines to overlay on those patterns using
KikuchiPatternSimulator.on_detector().To achieve this, the following main changes have been made:
EBSDDetector, which is used to describe the full orientation of the detector via the Euler angles (in degrees).EBSDDetector.euler[0]is the same asEBSDDetector.azimuthalandEBSDDetector.euler[1]is the same asEBSDDetector.tilt + 90, getters and setters forEBSDDetector.tilt,EBSDDetector.azimuthalandEBSDDetector.eulerhave been added, which ensure consistency with the other properties when setting one of them.EBSDDetector.__repr__().EBSDDetector, which are orientation matrices used to transform from CSs to CSd and the reverse. The matrix "u_s_inv" is used in the new functions for getting the direction cosines of the detector (see 3.).KikuchiPatternSimulator.on_detector()so that the euler angles of the detector are now used in calculating the orientation matrix "u_s_bruker". Previously, only theEBSDDetector.tiltseemed to be considered.EBSDDetectorand orientation matrices, which consider all three detector euler angles (previously only tilt and azimuthal were considered)._get_cosine_sine_of_alpha_and_azimuthal(),TestFitPatternDetectorOrientationto tests/test_signals/test_ebsd_master_pattern.py. This checks the fit between an EBSD pattern simulated from a master pattern and the associatedGeometricalKikuchiPatternSimulation. This seemed to be worth testing because with the current version of the functions to get the direction cosines from the detector, there was a rotation of the EBSD simulation from the master pattern compared to theGeometricalKikuchiPatternSimulationif both tilt and azimuthal were non-zero:Whereas with the new method for getting the direction cosines in this PR, the EBSD pattern and
GeometricalKikuchiPatternSimulationfit perfectly for any combination of detector euler angles:The entire kikuchipy test suite passes. I was not able to build the documentation on Windows but I think everything should be fine with the tutorial notebooks.
Progress of the #PR
Minimal example of the bug fix or new feature
For reviewers
__init__.py.section in
CHANGELOG.rst.kikuchipy/__init__.pyand.zenodo.json.