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pipeline work - #109
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pipeline work#109
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🟡 Changes recommended
The ROI generator has multiple execution-blocking defects, and WAXS percentile calculations incorrectly include masked pixels.
3 open findings
What changed in this PR
Adds geometry support, validation, tests, and coordinate guidance for the unified XPCS pipeline.
Changes:
- Adds geometry, ROI, mask, and plotting helpers.
- Adds synthetic pipeline tests across four scattering modes.
- Adds mask/ROI utilities and coordinate documentation.
| File | Description |
|---|---|
pyCHX/tests/test_xpcs_pipeline_geometry.py |
Tests geometry modes and pipeline outputs. |
pyCHX/_xpcs_pipeline_geometry.py |
Implements geometry and ROI helpers. |
pipelines/masking_and_rois/Detector_Masks_Add_Pixels.ipynb |
Adds detector-mask editing workflow. |
pipelines/masking_and_rois/Auto_ROI_Mask_Generator.ipynb |
Adds automatic ROI generation workflow. |
pipelines/COORDINATE_CONVENTIONS.md |
Documents detector coordinate conventions. |
pipelines/beam_center_position_issue.md |
Documents beam-center offsets. |
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| "try:\n", | ||
| " if mask_param_dict[mask_selection]['ang_centers']==None and mask_param_dict[mask_selection]['ang_width']==None and mask_param_dict[mask_selection]['inner_angle']==None and mask_param_dict[mask_selection]['outer_angle']==None and mask_param_dict[mask_selection]['num_angles']==None:\n", | ||
| " geometry='saxs'\n", | ||
| " roi_mask0, good_ind = combine_two_roi_mask( roi_mask0, np.ones(np.shape(roi_mask0),dtype=int),pixel_num_thres=pixel_num_thres) \n", | ||
| "except:\n", | ||
| " geometry='ang_saxs'\n", | ||
| " \n", |
| valid = np.asarray(mask, dtype=bool) & np.isfinite(smoothed) | ||
| if not valid.any(): | ||
| raise ValueError("No valid WAXS pixels") | ||
| values = smoothed[np.isfinite(smoothed)] |
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| The same conversion appears in the SAXS mask and ROI notebooks. It can shift beam masks, ROIs, and calibrated q maps. Separately, the unified pipeline writes SAXS result metadata with `beam_center_x` and `beam_center_y` swapped. | ||
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| **Check before changing historical results:** compare a direct-beam pixel in a raw frame, its BeamX/BeamY values, and its location in the oriented analysis image for each detector. The automatic finder is zero-based; manually entered centers may have a different convention. See [coordinate conventions](pipelines/COORDINATE_CONVENTIONS.md) for the full trace. |
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