samples/f005_simulation_data6_b0cc2a63__sample_000013/provenance.json

{
  "sample_uid": "f005_simulation_data6_b0cc2a63__sample_000013",
  "sample_name": "f005_simulation_data6_b0cc2a63__sample_000013",
  "original_sample_name": "sample_000013",
  "original_sample_id": "000013",
  "selection_rank": 2,
  "pool_index": 263,
  "source_index": 5,
  "source_file_name": "simulation_data6.hdf5",
  "source_file": "/gpfs/scratch/ailab/ai4physic/gendata3/simulation_data6.hdf5",
  "split": "test",
  "seed": 20260624,
  "sample_seed": 20260626,
  "hdf5_group": "/test/sample_000013",
  "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": 20260626,
    "dose_per_area_e_per_angstrom2": 1370170.314458269,
    "dose_range_e_per_angstrom2": [
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      1500000.0
    ],
    "scan_step_size_angstrom": 0.5299999713897705,
    "electrons_per_probe": 384880.7997783885,
    "charge_sharing_sigma_px": 0.22333286786118878,
    "charge_sharing_sigma_range_px": [
      0.2,
      0.5
    ],
    "read_noise_std_counts": 0.02021588415972253,
    "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": [
      2.8581411439301083e-19,
      6.0882066463818774e-05,
      0.004229934886097908
    ],
    "output_min_mean_max": [
      0.0,
      6.089553426136263e-05,
      0.004357500467449427
    ]
  },
  "ideal_potential_shape": [
    6,
    128,
    128
  ],
  "metadata": {
    "C10": -401.2518310546875,
    "C12": -13.184317588806152,
    "C21": 187.379150390625,
    "C23": -814.6881713867188,
    "C30": 10371734.0,
    "C32": 10346.3359375,
    "C34": -11791.021484375,
    "C41": -443766.78125,
    "C43": 234443.1875,
    "C45": -299696.40625,
    "C50": 12290260.0,
    "C52": -17827392.0,
    "C54": 1032114.5625,
    "C56": -15998074.0,
    "chromatic": 11545546.0,
    "crystal_type": "Hexagonal",
    "d_90": 9.55685043334961,
    "debye_temperature": 176.2496795654297,
    "energy_spread": 0.4009521007537842,
    "global_index": 5374,
    "ideal_potential_num_slices": 6,
    "material_id": "mp-19816",
    "material_key": "material_565",
    "num_probes": 9,
    "phi12": 1.2627971172332764,
    "phi21": 6.1266913414001465,
    "phi23": 4.398950099945068,
    "phi32": 5.872093200683594,
    "phi34": 2.031510829925537,
    "phi41": 5.793376445770264,
    "phi43": 0.9870206117630005,
    "phi45": 2.2419209480285645,
    "phi52": 5.760724067687988,
    "phi54": 6.221345901489258,
    "phi56": 1.3133814334869385,
    "phonon_seed": 1542359519,
    "probe_energy": 200000.0,
    "sample_id": 13,
    "scan_step_size": 0.5299999713897705,
    "semiangle_cutoff": 9.91810131072998,
    "source_size": 0.31555500626564026
  },
  "groundtruth_phase": {
    "source_ideal_potential_shape": [
      6,
      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": 0.5299999713897705,
    "valid_side_angstrom": 7.949999570846558,
    "valid_side_pixels_before_resize": 64,
    "valid_shape_before_resize": [
      64,
      64
    ],
    "target_shape": [
      41,
      41
    ],
    "resized_to_target_shape": true,
    "final_shape": [
      41,
      41
    ]
  },
  "groundtruth_note": "Ground truth was center-cropped/resized to exactly match PtyRAD fov='crop' phase shape.",
  "reconstruction_phase": {
    "object_phase_shape": [
      1,
      1,
      41,
      41
    ],
    "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": [
        80,
        120,
        80,
        120
      ],
      "probe_shape": [
        128,
        128
      ],
      "crop_shape": [
        41,
        41
      ],
      "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": [
      41,
      41
    ]
  },
  "metric_shape": [
    41,
    41
  ]
}