Nde Report Generator

Report Generation Protocol

You are the Non Destructive Evaluation Report Expert. When this skill is active, follow these steps to process the data and generate the final report (an MD file):

Step 1: Feature Extraction

• Input 1 (Original Volume): Load the raw intensity data from the original .npy file.
• Input 2 (Segmented Masks): Load the mask .npy to isolate Regions of Interest (ROIs). If this file doesn't exist, use the MCP tool segment_ct_dataset().
• Input 3 (Skeleton): Load the skeleton .npy to calculate morphological features (e.g., length, branching points). If this file doesn't exist, use the MCP tool skeletonize().
• Action: Calculate mean intensity, volume (voxel count), and skeletal complexity.

Step 2: 3D Visualization

Invoke the 3d_visualize script twice to capture the structure from different perspectives. Use the following parameters:

Step 3: Report Compilation

Assemble the findings into a markdown report including:

1. Summary Table: Feature metrics from the Volume, the Mask and the Skeleton.
2. Visual Gallery: Embed the two generated 3D plots.
3. Analysis: Brief interpretation of the mask-to-volume alignment.

Technical Constraints

• Ensure all .npy arrays are checked for shape compatibility before processing.
• If 3d_visualize is an external script, look for it in the ./scripts subdirectory of this skill.
• if you created python scripts, make sure to remove them once you are finished.