Generate Measurements from Synthetic Data

Overview

Use this skill when you have a 3D ground-truth (GT) volume and want to simulate what the microscope/system would measure, using precomputed system matrices (the forward operator $A$).

This is typically a prerequisite for solver development and benchmarking:

• GT volume ($x$): reconstruction.pt (or similar)
• system matrices ($A$): Interp_Vol_ID_*.pt files in a directory
• output measurements ($b = Ax$): saved as .tif images

Instructions

1. Prepare the ground-truth volume.

• Ensure the GT volume is a .pt file (for example reconstruction.pt).
• If your GT is stored in H5 format, convert it using scripts/convert_h5_to_pt.py.

2. Locate the forward model (A matrices).

• Identify the directory containing Interp_Vol_ID_*.pt.
• Confirm this directory corresponds to the same optical/system setup you want to simulate.

3. Pick/verify the crop (if needed).

• If the A volume extent is larger than your GT volume (or mismatched), set --crop-box-A.
• Format is x0 y0 z0 x1 y1 z1
• User would give the crop, or check crop in most related config/*.yaml. If you do not know how to crop, stop and ask user for help.

4. (Optional) Decide on noise injection.

• Use --noise-index to add noise to a specific measurement index.
• Use --noise-index -1 for clean measurement without noise.

5. Generate the measurements.

Run scripts/generate_bunny_measurements.py with:

• --gt-vol-path: path to GT .pt
• --raw-A-dir: path to the system matrices
• --output-dir: output folder for .tif measurements

What success looks like

You should consider this skill successful when:

• the script finishes without error, and
• output_dir contains one or more .tif measurement images, and
• (recommended) the images look plausible (non-empty, not all zeros/NaNs) when opened or visualized.

Examples

Example: generate noise-free measurements with A-cropping

Generate measurements from a GT volume using a specified system-matrix directory, and crop A to match the GT:

bash
1python scripts/generate_bunny_measurements.py \
2  --gt-vol-path data/synthetic/balls/case_1/reconstruction.pt \
3  --raw-A-dir data/raw/lightsheet_vol_6.9 \
4  --output-dir data/synthetic/balls/case_1/measurements \
5  --crop-box-A 5 268 18 69 332 82 \
6  --noise-index -1