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:

[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.