leonarski_f
680c36c20d
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* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
45 lines
3.3 KiB
Markdown
45 lines
3.3 KiB
Markdown
# IndexingSettings
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Settings for crystallography indexing
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## Properties
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Name | Type | Description | Notes
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------------ | ------------- | ------------- | -------------
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**algorithm** | [**IndexingAlgorithm**](IndexingAlgorithm.md) | | [default to IndexingAlgorithm.FFBIDX]
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**fft_max_unit_cell_a** | **float** | Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 250]
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**fft_min_unit_cell_a** | **float** | Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 10.0]
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**fft_high_resolution_a** | **float** | Sets how finely the FFT samples each search direction: it fixes the extent of the projection histogram, and with it the transform size, so it affects execution time and memory of FFT. It does NOT filter spots - every spot is projected whatever its resolution, so raising it does not make the transform see a coarser subset of the data. There is also correlation between smallest unit cell and this value, which need to be checked for very small systems. | [default to 2.0]
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**fft_num_vectors** | **int** | Number of search directions for the FFT algorithm; parameter value affects execution time of FFT. | [default to 16384]
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**tolerance** | **float** | Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted |
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**thread_count** | **int** | Thread count for indexing algorithm |
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**geom_refinement_algorithm** | [**GeomRefinementAlgorithm**](GeomRefinementAlgorithm.md) | |
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**unit_cell_dist_tolerance** | **float** | Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored | [default to 0.05]
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**viable_cell_min_spots** | **int** | Minimum number of indexed spots required for a cell to be considered viable | [default to 10]
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**index_ice_rings** | **bool** | Include spots marked as ice rings in the indexing run. If `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing. | [default to False]
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**rotation_indexing** | **bool** | | [default to False]
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**rotation_indexing_min_angular_range_deg** | **float** | | [default to 20.0]
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**rotation_indexing_angular_stride_deg** | **float** | | [default to 0.5]
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**blocking** | **bool** | Indexing in Jungfraujoch goes with a dedicated thread pool. If set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates. If set to true, the thread pool will block until a thread is available. | [default to True]
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## Example
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```python
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from jfjoch_client.models.indexing_settings import IndexingSettings
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# TODO update the JSON string below
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json = "{}"
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# create an instance of IndexingSettings from a JSON string
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indexing_settings_instance = IndexingSettings.from_json(json)
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# print the JSON string representation of the object
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print(IndexingSettings.to_json())
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# convert the object into a dict
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indexing_settings_dict = indexing_settings_instance.to_dict()
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# create an instance of IndexingSettings from a dict
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indexing_settings_from_dict = IndexingSettings.from_dict(indexing_settings_dict)
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```
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[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
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