Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: generalize AR calculations, chi center, polarizations, reflections #133

Open
BijalBPatel opened this issue Apr 10, 2024 · 1 comment · May be fixed by #147
Open

feat: generalize AR calculations, chi center, polarizations, reflections #133

BijalBPatel opened this issue Apr 10, 2024 · 1 comment · May be fixed by #147
Assignees
@BijalBPatel
Labels
enhancement New feature or request

Comments

@BijalBPatel
Copy link
Collaborator

BijalBPatel commented Apr 10, 2024 •
edited
Loading

Proposed changes:

  1. Generalize Calculation beyond para, perp, and polarization framing. Allow parameters chi_1, chi_2 as optional parameters to choose where the chi wedges are centered. Default behavior will be chi_1 = 0, chi_2 = chi1 - 90, but allow users to override this. This enables more flexibility e.g., computing AR along a target chi aligned with a biaxial director, or sanity check of calculating AR aligned 45 degrees to uniaxial director. Goal is for default behavior to match current behavior.
  2. Add a flag to integrate 4 chi wedges per image, instead of 2. Presently, AR is calculated from two chi-wedges, centered on 0 +- chi_width (para) and -90 +- chi_width (perp). The proposed change would allow incorporating the reflection (so I_para is calculated from the wedges centered on 0 and 180, and I_perp is from wedges centered on 90 and -90).

Possible QOL additions:

  • Warn if chi_1 and chi_2 are not perpendicular
  • Warn if any wedges are overlapping
  • Add a flag to enable inferring chi_1 and chi_2 from polarization metadata

Possible Connections with existing issues:

Existing Code for reference:

PyHyperScattering/src/PyHyperScattering/RSoXS.py

Lines 109 to 151 in 6603dd4

def AR(self,calc2d=False,two_AR=False,chi_width=5,calc2d_norm_energy=None):
'''
Calculate the RSoXS Anisotropic Ratio (AR) of either a single RSoXS scan or a polarized pair of scans.
AR is defined as (para-perp)/(para+perp) where para is the chi slice parallel to the polarization direction, and perp is the chi slice 90 deg offset from the polarization direction.
Args:
img (xarray): image to plot
calc2d (bool): calculate the AR using both polarizations
two_AR (bool): return both polarizations if calc2d = True. If two_AR = False, return the average AR between the two polarizations.
calc2d_norm_energy (numeric): if set, normalizes each polarization's AR at a given energy. THIS EFFECTIVELY FORCES THE AR TO 0 AT THIS ENERGY.
chi_width (int, default 5): the width of chi slices used in calculating AR.
'''
if(not calc2d):
para = self.slice_chi(0,chi_width=chi_width)
perp = self.slice_chi(-90,chi_width=chi_width)
return ((para - perp) / (para+perp))
elif(calc2d):
para_pol = self.select_pol(0)
perp_pol = self.select_pol(90)
para_para = para_pol.rsoxs.slice_chi(0,chi_width=chi_width)
para_perp = para_pol.rsoxs.slice_chi(-90,chi_width=chi_width)
perp_perp = perp_pol.rsoxs.slice_chi(-90,chi_width=chi_width)
perp_para = perp_pol.rsoxs.slice_chi(0,chi_width=chi_width)
AR_para = ((para_para - para_perp)/(para_para+para_perp))
AR_perp = ((perp_perp - perp_para)/(perp_perp+perp_para))
if calc2d_norm_energy is not None:
AR_para = AR_para / AR_para.sel(energy=calc2d_norm_energy)
AR_perp = AR_perp / AR_perp.sel(energy=calc2d_norm_energy)
if (AR_para < AR_perp).all() or (AR_perp < AR_para).all():
warnings.warn('One polarization has a systematically higher/lower AR than the other. Typically this indicates bad intensity values.',stacklevel=2)
if two_AR:
return (AR_para,AR_perp)
else:
return (AR_para+AR_perp)/2
else:
raise NotImplementedError('Need either a single DataArray or a list of 2 dataarrays')

@BijalBPatel BijalBPatel added the enhancement New feature or request label Apr 10, 2024
@BijalBPatel BijalBPatel self-assigned this Apr 10, 2024
@BijalBPatel BijalBPatel changed the title feat generalize AR calculations, chi center, polarizations, reflections feat: generalize AR calculations, chi center, polarizations, reflections Apr 10, 2024
@BijalBPatel
Copy link
Collaborator Author

BijalBPatel commented Apr 26, 2024 •
edited
Loading

Branch is feature complete, but there are some additions I want to make before PR.

  • Tutorial
  • Aggressive Testing on meaningful uniaxial datasets
  • Automated Tests
  • Redoing the logic to pull integration wedges into a helper function. Right now the code logic is unnecessarily muddy and intelligent selection selection of chi,q wedges is a useful thing on its own. This change is unlikely to be visible to function users, but it will make testing easier/ more robust.

At the earliest, i'll work on it again next Tuesday, but its open to anyone to test.

@cbishop4 cbishop4 linked a pull request Sep 4, 2024 that will close this issue
133 feat generalize ar calculations chi center polarizations reflections #147
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@BijalBPatel BijalBPatel

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

133 feat generalize ar calculations chi center polarizations reflections usnistgov/PyHyperScattering
1 participant
@BijalBPatel