AutoScriptCopilot/tem_workflow.yaml at main · xyin-anl/AutoScriptCopilot · GitHub

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name: TEMWorkflow_12_17_2024_22_15_45
state_defs:
- current_node_type: str
- previous_node_type: str
- human_input: str
- input: str
- output: str
- messages: List[dict]
- microscope_id: str
- microscope_info: Dict[str, str]
- vacuum_state: str
- beam_state: bool
- detector_status: Dict[str, bool]
- magnification: float
- focus: float
- stigmator_values: Dict[str, float]
- exposure_time: float
- frame_size: int
- detector_type: str
- trial_mode: bool
- direct_mode: bool
- recommender_knowledge: str
- data_analysis_tool: str
- trial_mode_detector_type: str
- current_image: str
- image_quality_metrics: Dict[str, float]
- optimization_history: List[dict]
- validation_response: dict
- updated_parameters: dict
- data_analysis_results: dict
nodes:
  initialize:
    type: initialize
    sink:
    - microscope_id
    - microscope_info
    - vacuum_state
    - beam_state
    - detector_status
    next: validate
  validate:
    type: prompt
    template: 'Analyze microscope setup: Vacuum State: {vacuum_state} Beam State:
      {beam_state} Detector Status: {detector_status} Validate against required conditions:
      1. Vacuum must be in READY state 2. Beam must be active and properly controlled
      3. Selected detector must be operational Output validation results as JSON:
      {{ "is_valid": bool, "issues": [str], "recommendations": [str] }}'
    sink: validation_response
    next:
      condition: validation_response["is_valid"]
      then: recommend
      otherwise: END
  recommend:
    type: prompt
    template: 'Recommender knowledge: {recommender_knowledge} Current microscope state
      and setup: - Vacuum State: {vacuum_state} - Beam State: {beam_state} - Detector
      Type: {detector_type} Recommend optimal imaging parameters for the current setup.
      Consider: 1. Detector capabilities and limitations 2. Sample preservation requirements
      3. Image quality requirements Output as JSON: {{ "parameter_values": {{ "magnification":
      float, "focus": float, "exposure_time": float, "frame_size": int }}, "reasoning":
      str }}'
    sink: updated_parameters
    next: confirm
  acquire:
    type: acquire
    sink: current_image
    next:
      condition: not direct_mode
      then: assess
      otherwise: analyze
  align:
    type: align
    sink: [focus, stigmator_values]
    next: acquire
  assess:
    type: prompt
    template: 'Analyze the TEM image quality: Current Settings: - Magnification: {magnification}
      - Focus: {focus} - Stigmator Values: {stigmator_values} - Frame Size: {frame_size}
      - Exposure: {exposure_time} Evaluate image for: 1. Focus quality (check Fresnel
      fringes, edge sharpness) 2. Astigmatism correction 3. Brightness and contrast
      4. Signal-to-noise ratio 5. Stage drift effects 6. Beam damage indicators Output
      analysis as JSON: {{ "quality_score": float (0-10), "issues": [ {{ "type": str,
      "severity": str, "description": str }} ], "improvements": [ {{ "parameter":
      str, "suggestion": str, "reasoning": str }} ] }}'
    sink: image_quality_metrics
    image_keys: current_image
    next:
      condition: image_quality_metrics["quality_score"] < 8.0
      then: align
      otherwise: optimize
  optimize:
    type: prompt
    template: 'Review current imaging performance: Quality Metrics: {image_quality_metrics}
      Optimization History: {optimization_history} Current Parameters: - Magnification:
      {magnification} - Focus: {focus} - Stigmator Values: {stigmator_values} - Exposure
      Time: {exposure_time} - Frame Size: {frame_size} Suggest parameter adjustments
      to improve image quality. Consider: 1. Previous optimization attempts 2. Quality
      improvement trends 3. Physical limits of the system Output as JSON: {{ "parameter_values":
      {{ "magnification": float, "focus": float, "exposure_time": float, "frame_size":
      int }}, "reasoning": str, "stop_optimization": bool }}'
    sink: updated_parameters
    next:
      condition: not updated_parameters["stop_optimization"]
      then: confirm
      otherwise: analyze
  confirm:
    type: confirm
    sink:
    - magnification
    - focus
    - exposure_time
    - frame_size
    - trial_mode
    - direct_mode
    - detector_type
    next: acquire
  analyze:
    type: analyze
    sink: data_analysis_results
    next: END
entry_point: initialize
llm: gpt-4o
vlm: gpt-4o
exit_commands: [stop workflow, quit workflow, terminate workflow]
checkpointer: memory