ptychography-on-sem

id	ptychography_on_sem
name	Ptychography on SEM
description	A compound skill that first acquires data on the SEM and then processes it using the ptychography workflow.
version	1.0.0

Agents Involved

• agent_sem
• agent_ptychography

Required Tools

• This is a compound skill. The planner must call read_skill_content for acquire_4d_stem and ptychography before drafting the plan.
• For SEM acquisition, use exactly the tools and argument shapes listed in the acquire_4d_stem skill.
• For ptychography reconstruction, use exactly the tools and argument shapes listed in the ptychography skill.
• Do not add tools that are not listed by those two referenced skills.

Steps

1. Acquire SEM Data: Expand the full acquire_4d_stem skill steps into this plan, preserving its tool order and required user-confirmation gates.
2. Process Ptychography: Expand the full ptychography skill steps after acquisition, using the acquired 4D-STEM data path when a ptychography step requires experimental data.

Planning Contract

• The planner must expand referenced skills into concrete PlanSteps. Do not leave a high-level "run acquire_4d_stem" or "run ptychography" placeholder step.
• Do not insert SEM state checks, existing-data checks, skip-acquisition prompts, scan-parameter calculation steps, ROI confirmation tools, final validation steps, or extra waits unless one of the referenced skills explicitly lists them.
• Do not use agent_sem.get_sem_state or agent_sem.calculate_scan_parameters for this compound workflow unless the user explicitly asks for those as a separate requirement.
• If the user explicitly says they already have selected/ready 4D-STEM data and wants to skip acquisition, omit the acquire_4d_stem skill and plan only the ptychography skill. Do not add an SEM state check to decide this.
• The output of SEM acquisition may be referenced by later ptychography steps as a placeholder such as {{acquire_4d_stem.data_path}} when the exact data path is not known at planning time.

Success Criteria

• 4D-STEM data is acquired.
• Ptychography parameters are validated and saved.
• Reconstruction job is submitted.

Failure Policy

• If SEM acquisition fails, stop before reconstruction.
• If reconstruction parameters are missing, ask the user before submitting.