# Dataset INI files

Every dataset has an `.ini` file that lives alongside its `.h5` file in the dataset folder. It is created automatically when you import a dataset and updated by the GUI each time you save settings in a processing step. You rarely need to edit it by hand, but understanding its structure helps when diagnosing problems or running COSEDA programmatically.

The file has four sections:

```ini
[Paths]
geomfile_path = indexingintegration_20260525_145631/geometry.geom
cellfile_path = indexingintegration_20260525_145631/cellfile.cell

[AcquisitionDetails]
acquisition_start = 1741607077
acquisition_end = 1741607077
instrument_manufacturer = FEI Company
instrument_model = Titan
instrument_id = 3862
detector_used = BM-Ceta
acceleration_voltage = 300000
camera_length = 0.60799999999999998
pixel_width = 26747691.052856494
pixel_height = 26747691.052856494
binning_width = 4
binning_height = 4
resolution_width = 4096
resolution_height = 4096
exposure_time = 0.052607000000000001
pixel_unit = 1/m
pixel_offset_x = -13694817819.062525
pixel_offset_y = -13694817819.062525
pixels_per_meter = 17857.14285714286
camera_length_correction = 1.78
adu_per_photon = 5

[Parameters]
sample_class = MOF
h5conversion_limit_frames = False
h5conversion_bin_factor = 1
peakfinding_threshold = 40
peakfinding_min_snr = 5.0
peakfinding_min_pix_count = 4
peakfinding_max_pix_count = 500
peakfinding_local_bg_radius = 10
peakfinding_min_res = 20
peakfinding_max_res = 500
peakfinding_x0 = 510
peakfinding_y0 = 512
centerfinding_tolerance = 5
centerfinding_min_peaks = 40
centerfinding_resolution_limit = 150
centerfinding_min_samples_fraction = 0.1
centerfinding_x0 = 510
centerfinding_y0 = 512
centerrefinement_tolerance = 5
centerrefinement_min_peaks = 50
centerrefinement_resolution_limit = 300
centerrefinement_max_iterations = 20
centerrefinement_convergence_threshold = 0.1
centerfinding_batch_size = 1000
strip_threshold = 20
strip_force = True
atlas_backlash_offset_um = 0.0
centerfinding_force_linear_fit = True
centerrefinement_method = Beamstop
xgandalf_tolerance = 5,5,5,1.5
xgandalf_sampling_pitch = 5
xgandalf_min_lattice_vector_length = 3
xgandalf_max_lattice_vector_length = 30
xgandalf_grad_desc_iterations = 2
tolerance_5d = 0.2
fix_profile_radius = True
peakfinding_algorithm = peakfinder8
centerfinding_dbscan_eps = 5.0
centerfinding_skip_linear_fit = False
centerrefinement_deviation_aggregation = median
centerrefinement_lowess_frac = 0.1

[Output]
```

## [Paths]

The `.h5` and `.ini` share the same base name in the same folder, so COSEDA derives all file locations from that base name automatically. The only keys written here by the GUI are:

| Key | Description |
|---|---|
| `geomfile_path` | Path to the CrystFEL geometry file last used for indexing. Written when indexing settings are saved; read by the merge window to locate the cell. |
| `cellfile_path` | Path to the cell file last used for indexing. Written and read for the same reasons as `geomfile_path`. |

## [AcquisitionDetails]

Instrument and detector metadata read from the raw file header during import. These values drive physical calculations throughout the pipeline (detector shifts, geometry export, MTZ export).

| Key | Description |
|---|---|
| `acceleration_voltage` | Electron accelerating voltage (V). |
| `camera_length` | Nominal camera length (m). |
| `camera_length_correction` | Correction factor applied to the nominal camera length. |
| `pixels_per_meter` | Detector pixel scale (px/m), derived from `pixel_width` / `binning_width`. Used to convert beam center offsets to detector shifts in mm. |
| `adu_per_photon` | ADU conversion factor for the detector. |
| `resolution_width`, `resolution_height` | Full detector size in pixels (before binning). |
| `binning_width`, `binning_height` | Hardware binning factors. |

## [Parameters]

All processing parameters for this dataset. The GUI appends or overwrites keys in this section each time you click **Save Settings** in a processing step. Keys are grouped by prefix:

| Prefix | Stage |
|---|---|
| `h5conversion_*` | Import / HDF5 conversion |
| `peakfinding_*` | Peak finding |
| `strip_*` | Strip HDF5 (remove empty frames) |
| `atlas_*` | Atlas reconstruction and display |
| `centerfinding_*` | Center finding |
| `centerrefinement_*` | Center refinement |
| `xgandalf_*`, `tolerance_*`, `fix_profile_radius`, … | Indexing & integration |

Parameters that are not yet set for a given step are simply absent from this section; the corresponding stage will refuse to run until required keys are present.

`atlas_backlash_offset_um` is optional. It stores the horizontal offset, in micrometres, applied to left-going scan streaks during atlas reconstruction. A value of `0.0` disables the correction. The correction is applied when the atlas is built; raw stage-position datasets in the HDF5 file are not overwritten.

## [Output]

Currently not used.