small feature addition: use probe intensity for com shift

[a4894z]

Features/fixes

The default behavior is to use the 0th order shared probe mode to compute the center of mass (com); this adds the option of using the probe intensity as well.

Related issues (optional)

N/A

Mentions

Ming Du

Checklist

Have you...

• Formatted your code properly adhering to PEP-8? Considering using RUFF to format your code automatically.
• Resolved all merge conflicts with the main branch?
• Checked the diffs between your branch and the main branch to ensure that your changes are not introducing any regressions or unnecessary/irrelevant changes?

[Copilot]

Pull Request Overview

This PR adds a toggle to compute the probe’s center of mass using its intensity rather than always using the default (0th order shared) probe mode.

• Introduces use_intensity_for_com option in ProbeCenterConstraintOptions.
• Updates center_probe to branch on that option and compute intensity‐based COM when enabled.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
src/ptychi/api/options/base.py	Added use_intensity_for_com flag with a docstring to ProbeCenterConstraintOptions.
src/ptychi/data_structures/probe.py	Modified center_probe to optionally compute COM from probe intensity.

Comments suppressed due to low confidence (3)

src/ptychi/api/options/base.py:505

• Clarify the docstring to state that enabling this flag computes COM from the probe’s squared‐magnitude intensity, and ensure the indentation matches surrounding fields.

use_intensity_for_com: bool = False

src/ptychi/data_structures/probe.py:398

• Add a unit test for the intensity‐based centering branch to verify the COM shift is computed correctly when use_intensity_for_com is enabled.

if self.options.center_constraint.use_intensity_for_com:

src/ptychi/data_structures/probe.py:399

• Computing intensity directly on self.data[0,...] bypasses any operator mode transformations applied by get_mode_and_opr_mode. Consider using get_mode_and_opr_mode(0, 0) inside the intensity calculation to stay consistent with the default COM computation.

probe_to_be_shifted = torch.sum( torch.abs( self.data[0,...] ) ** 2, 0 )

[Copilot]

[nitpick] Remove extra spaces inside the torch.sum and torch.abs calls to match project style (torch.sum(torch.abs(self.data[0,...])**2, dim=0)).

Suggested change

	probe_to_be_shifted = torch.sum( torch.abs( self.data[0,...] ) ** 2, 0 )
	probe_to_be_shifted = torch.sum(torch.abs(self.data[0,...]) ** 2, 0)