Chocopy/PtychoFlow_DiT

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

Metrics are computed only after groundtruth.shape == reconstruction.shape, then both images are independently min-max scaled to [0, 1].