| --- |
| license: mit |
| tags: |
| - ptyrad |
| - 4dstem |
| - ptychography |
| - electron-microscopy |
| --- |
| |
| # PtyRAD reconstruction eval on generated test split |
|
|
| This folder contains PtyRAD reconstructions for a seeded random subset of `test` samples pooled from multiple HDF5 files. |
|
|
| ## Dataset files |
|
|
| - `simulation_data1.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data1.hdf5` |
| - `simulation_data2.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data2.hdf5` |
| - `simulation_data3.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data3.hdf5` |
| - `simulation_data4.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data4.hdf5` |
| - `simulation_data5.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data5.hdf5` |
| - `simulation_data6.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data6.hdf5` |
| - `simulation_data7.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data7.hdf5` |
| - `simulation_data8.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data8.hdf5` |
| - `simulation_data_aug1.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data_aug1.hdf5` |
| - `simulation_data_aug2.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data_aug2.hdf5` |
| - `simulation_data_aug3.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data_aug3.hdf5` |
| - `simulation_data_aug4.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data_aug4.hdf5` |
| - `simulation_data_aug5.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data_aug5.hdf5` |
| - `simulation_data1.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data1.hdf5` |
| - `simulation_data2.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data2.hdf5` |
| - `simulation_data3.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data3.hdf5` |
| - `simulation_data4.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data4.hdf5` |
| - `simulation_data5.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data5.hdf5` |
| - `simulation_data_aug1.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data_aug1.hdf5` |
| - `simulation_data_aug2.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data_aug2.hdf5` |
| - `simulation_data_aug3.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data_aug3.hdf5` |
| - `simulation_data_aug4.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data_aug4.hdf5` |
| - `simulation_data_aug5.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_01/simulation_data_aug5.hdf5` |
| - `simulation_data10.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data10.hdf5` |
| - `simulation_data11.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data11.hdf5` |
| - `simulation_data7.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data7.hdf5` |
| - `simulation_data8.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data8.hdf5` |
| - `simulation_data9.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data9.hdf5` |
| - `simulation_data_aug10.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data_aug10.hdf5` |
| - `simulation_data_aug11.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data_aug11.hdf5` |
| - `simulation_data_aug7.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data_aug7.hdf5` |
| - `simulation_data_aug8.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data_aug8.hdf5` |
| - `simulation_data_aug9.hdf5`: `/gpfs/scratch/ailab/ai4physic/gendata3_std_02/simulation_data_aug9.hdf5` |
| - `simulation_data1.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data1.hdf5` |
| - `simulation_data2.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data2.hdf5` |
| - `simulation_data3.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data3.hdf5` |
| - `simulation_data4.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data4.hdf5` |
| - `simulation_data5.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data5.hdf5` |
| - `simulation_data_aug1.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data_aug1.hdf5` |
| - `simulation_data_aug2.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data_aug2.hdf5` |
| - `simulation_data_aug3.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data_aug3.hdf5` |
| - `simulation_data10_cp.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data10_cp.hdf5` |
| - `simulation_data11.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data11.hdf5` |
| - `simulation_data12.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data12.hdf5` |
| - `simulation_data6.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data6.hdf5` |
| - `simulation_data7.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data7.hdf5` |
| - `simulation_data8.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data8.hdf5` |
| - `simulation_data9.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data9.hdf5` |
| - `simulation_data_aug6.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data_aug6.hdf5` |
| - `simulation_data_aug7.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data_aug7.hdf5` |
| - `simulation_data_aug8.hdf5`: `/gpfs/scratch/ailab/ai4physic/c30_small_std02/simulation_data_aug8.hdf5` |
|
|
| ## Selection |
|
|
| - split: `test` |
| - seed for sample selection: `20260624` |
| - requested samples: `10` |
| - available samples across all files: `1933` |
| - actual selected samples: `10` |
| - selection manifest CSV: `selected_samples.csv` |
| - selection manifest JSON: `selected_samples.json` |
| - selection manifest JSONL: `selected_samples.jsonl` |
|
|
| The manifest records `source_file`, `source_file_name`, `split`, `original_sample_name`, `original_sample_id`, `pool_index`, `selection_rank`, and `sample_uid`. |
|
|
| ## Reconstruction and metrics |
|
|
| - PtyRAD iterations per sample: `100` |
| - PtyRAD object: `obj_Nlayer=1`, `obj_omode_max=1` |
| - measurement calibration: `meas_calibration.mode=kMax`, `value=2.5` 1/Angstrom when positive |
| - measurement noise: `enabled=True`, dose sampled uniformly from `100000.0` to `1500000.0` e-/Angstrom^2 |
| - metrics file: `metrics.csv` |
|
|
| For each selected sample, the script saves: |
|
|
| - `groundtruth.png`: min-max PNG from the center valid phase crop, resized to the PtyRAD scanned-FOV crop shape |
| - `reconstruction.png`: min-max PNG from PtyRAD `objp[0, 0]` with `Analyzer.get_object_phase(fov="crop")` |
| - `provenance.json`: includes the sampled dose, charge-sharing sigma, read-noise std, and GT/recon crop metadata |
| - `ptyrad_params.yaml` or `.json`: params used by `ptyrad run` |
| - `ptyrad.log`: stdout/stderr from PtyRAD |
| - `model_iter*.hdf5`: PtyRAD output checkpoint, inside the per-sample reconstruction directory when available |
|
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| Metrics are computed only after `groundtruth.shape == reconstruction.shape`, then both images are independently min-max scaled to `[0, 1]`. |
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