samples/f034_simulation_data2_770bee21__sample_000031/provenance.json

{
  "sample_uid": "f034_simulation_data2_770bee21__sample_000031",
  "sample_name": "f034_simulation_data2_770bee21__sample_000031",
  "original_sample_name": "sample_000031",
  "original_sample_id": "000031",
  "selection_rank": 6,
  "pool_index": 1286,
  "source_index": 34,
  "source_file_name": "simulation_data2.hdf5",
  "source_file": "/gpfs/scratch/ailab/ai4physic/c30_small/simulation_data2.hdf5",
  "split": "test",
  "seed": 20260624,
  "sample_seed": 20260630,
  "hdf5_group": "/test/sample_000031",
  "measurement_shape": [
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    16,
    128,
    128
  ],
  "raw_measurement_shape": [
    16,
    16,
    128,
    128
  ],
  "measurement_noise": {
    "enabled": true,
    "profile": "pretrain_physical_noise_for_ptyrad_intensity",
    "note": "Applied Poisson + charge sharing + read noise + nonnegative clamp; skipped pretrain sqrt/z-score so PtyRAD receives nonnegative intensities.",
    "sample_seed": 20260630,
    "dose_per_area_e_per_angstrom2": 662363.7659548009,
    "dose_range_e_per_angstrom2": [
      100000.0,
      1500000.0
    ],
    "scan_step_size_angstrom": 0.32693320512771606,
    "electrons_per_probe": 70796.96348789154,
    "charge_sharing_sigma_px": 0.3575963783378047,
    "charge_sharing_sigma_range_px": [
      0.2,
      0.5
    ],
    "read_noise_std_counts": 0.020057850486180497,
    "read_noise_std_range_counts": [
      0.02,
      0.05
    ],
    "charge_sharing_weak_threshold": 20,
    "charge_sharing_radius": 2,
    "charge_sharing_image_chunk_size": 256,
    "charge_sharing_event_chunk_size": 100000,
    "noise_device": "cuda",
    "input_min_mean_max": [
      3.018520866452542e-19,
      6.09802154940553e-05,
      0.004164824262261391
    ],
    "output_min_mean_max": [
      0.0,
      6.107737135607749e-05,
      0.004434080328792334
    ]
  },
  "ideal_potential_shape": [
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    128,
    128
  ],
  "metadata": {
    "C10": -17.336061477661133,
    "C12": -26.86164093017578,
    "C21": 336.6799011230469,
    "C23": -121.27379608154297,
    "C30": 3645067.75,
    "C32": -5922.4150390625,
    "C34": -3966.7568359375,
    "C41": -220474.015625,
    "C43": -387137.1875,
    "C45": -187434.875,
    "C50": 280867296.0,
    "C52": -12314225.0,
    "C54": 10058172.0,
    "C56": 13698078.0,
    "chromatic": 14631543.0,
    "crystal_type": "Cubic",
    "d_90": 6.939780235290527,
    "debye_temperature": 695.6400756835938,
    "energy_spread": 0.3843620717525482,
    "global_index": 1658,
    "ideal_potential_num_slices": 7,
    "material_id": "mp-961650",
    "material_key": "material_1658",
    "num_probes": 10,
    "phi12": 5.521120548248291,
    "phi21": 1.9006394147872925,
    "phi23": 5.610154151916504,
    "phi32": 3.1347808837890625,
    "phi34": 3.6065073013305664,
    "phi41": 4.919930934906006,
    "phi43": 4.581060409545898,
    "phi45": 0.274361252784729,
    "phi52": 0.7832724452018738,
    "phi54": 2.1448049545288086,
    "phi56": 3.7781665325164795,
    "phonon_seed": 1881615466,
    "probe_energy": 200000.0,
    "sample_id": 31,
    "scan_step_size": 0.32693320512771606,
    "semiangle_cutoff": 9.28663158416748,
    "source_size": 0.3762793242931366
  },
  "groundtruth_phase": {
    "source_ideal_potential_shape": [
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      128,
      128
    ],
    "full_2d_shape": [
      128,
      128
    ],
    "canonical_center_crop_pixels": 64,
    "canonical_shape": [
      64,
      64
    ],
    "valid_scan_intervals": 15,
    "phase_build_extent_angstrom": 15.9,
    "phase_build_pixels": 128,
    "phase_pixel_size_angstrom": 0.12421875,
    "scan_step_size_angstrom": 0.32693320512771606,
    "valid_side_angstrom": 4.903998076915741,
    "valid_side_pixels_before_resize": 39,
    "valid_shape_before_resize": [
      39,
      39
    ],
    "target_shape": [
      26,
      26
    ],
    "resized_to_target_shape": true,
    "final_shape": [
      26,
      26
    ]
  },
  "groundtruth_note": "Ground truth was center-cropped/resized to exactly match PtyRAD fov='crop' phase shape.",
  "reconstruction_phase": {
    "object_phase_shape": [
      1,
      1,
      26,
      26
    ],
    "phase_reduction": "single object mode, single slice: arr[0, 0]",
    "source": "ptyrad.analysis.Analyzer.get_object_phase",
    "fov": "crop",
    "fov_info": {
      "fov_bbox_ymin_ymax_xmin_xmax": [
        78,
        103,
        79,
        104
      ],
      "probe_shape": [
        128,
        128
      ],
      "crop_shape": [
        26,
        26
      ],
      "crop_rule": "center positions = crop_pos + probe_shape // 2; bbox bounds are inclusive"
    },
    "model_attributes": {
      "dx": 0.20000000298023224,
      "dk": 0.0390625,
      "meas_Npix": 128,
      "simu_Npix": 128,
      "slice_thickness": 20.0
    },
    "final_2d_shape": [
      26,
      26
    ]
  },
  "metric_shape": [
    26,
    26
  ]
}