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still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it

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The stills distance is found from the data, so the --detector-distance pins go. Ice-ring detection,
the polarisation degree on one Rayonix set, the geometry pre-pass switch-off and the Alvra/one AGIPD
gains are no longer given: each was neutral or better without it. Kept: --wavelength where the file
states none or a different one, the polarisation on the mixed-form set (its beam-stop mask depends on
it) and the gain of one AGIPD set whose frames carry an uncorrected baseline.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
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leonarski_fandClaude Opus 5.5 committed 2026-10-22 22:13:53 +02:00
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tools/battery/still_manifest.json
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@@ -3,15 +3,15 @@
{"id": "sacla243", "cxidb": 243, "facility": "SACLA", "beamline": "BL2", "detector": "MPCCD (8 panels, 50 um)", "format": "Cheetah-SACLA HDF5", "pdb": "31JT", "sg": "P 2 21 21", "d_cut": 1.63, "r_free_deposited": 0.1943, "images_deposited": 52151, "inputs": ["sacla_243/raw_all/run*.h5"], "args": ["-C", "39.36,79.16,145.40,90,90,90", "-S", "P 2 21 21"], "tiers": {}},
{"id": "sacla237", "cxidb": 237, "facility": "SACLA", "beamline": "BL2", "detector": "MPCCD (8 panels, 50 um)", "format": "Cheetah-SACLA HDF5", "pdb": "9S06", "sg": "P 21 21 21", "d_cut": 2.05, "r_free_deposited": 0.219, "images_deposited": null, "inputs": ["sacla_237/raw/run13063[7-9]-*.h5", "sacla_237/raw/run13064[0-2]-*.h5"], "args": ["-C", "64.80,71.09,207.26,90,90,90", "-S", "P212121"], "tiers": {}},
{"id": "sacla236", "cxidb": 236, "facility": "SACLA", "beamline": "BL2", "detector": "MPCCD (8 panels, 50 um)", "format": "Cheetah-SACLA HDF5", "pdb": "9V3D", "sg": "P 43 21 2", "d_cut": 1.68, "r_free_deposited": 0.2252, "images_deposited": 16083, "inputs": ["sacla_236/raw/run157*.h5"], "args": ["-C", "79.45,79.45,38.15,90,90,90", "-S", "P43212"], "tiers": {"smoke": {"images": 2000}}},
{"id": "pal86", "cxidb": 86, "facility": "PAL-XFEL", "beamline": "NCI", "detector": "Rayonix MX225-HS (4x4 binned, 156 um)", "format": "Cheetah CXI", "pdb": "6IG7", "sg": "P 61 2 2", "d_cut": 1.8, "r_free_deposited": 0.2024, "images_deposited": null, "inputs": ["pal_86/raw/*.cxi", "pal_86/raw_more/*.cxi"], "args": ["--detector-distance", "105", "--detect-ice-rings=on", "-C", "92.663,92.663,128.591,90,90,120", "-S", "P6122"], "tiers": {}},
{"id": "pal86", "cxidb": 86, "facility": "PAL-XFEL", "beamline": "NCI", "detector": "Rayonix MX225-HS (4x4 binned, 156 um)", "format": "Cheetah CXI", "pdb": "6IG7", "sg": "P 61 2 2", "d_cut": 1.8, "r_free_deposited": 0.2024, "images_deposited": null, "inputs": ["pal_86/raw/*.cxi", "pal_86/raw_more/*.cxi"], "args": ["-C", "92.663,92.663,128.591,90,90,120", "-S", "P6122"], "tiers": {}},
{"id": "pal90", "cxidb": 90, "facility": "PAL-XFEL", "beamline": "NCI", "detector": "Rayonix MX225-HS (4x4 binned, 156 um)", "format": "Cheetah CXI", "pdb": "6IRK", "sg": "I 2 2 2", "d_cut": 1.75, "r_free_deposited": 0.203, "images_deposited": null, "inputs": ["pal_90/raw/*.cxi"], "args": ["-C", "93.050,99.000,101.920,90,90,90", "-S", "I222"], "tiers": {"smoke": {"images": 1500}}},
{"id": "lcls222", "cxidb": 222, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "8TDQ", "sg": "P 65 2 2", "d_cut": 1.65, "r_free_deposited": 0.2012, "images_deposited": null, "inputs": ["lcls_222/xtc/*.xtc", "lcls_222/xtc_more/*.xtc"], "args": ["--detector-distance", "193.43", "--polarization", "0.998", "-C", "78.616,78.616,265.275,90,90,120", "-S", "P6522"], "tiers": {"smoke": {"images": 1500}}},
{"id": "lcls242_s", "cxidb": 242, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "9O4S", "sg": "P 1 21 1", "d_cut": 1.95, "r_free_deposited": 0.2102, "images_deposited": null, "inputs": ["lcls_242/xtc/*.xtc", "lcls_242/xtc_more/*.xtc"], "args": ["--detector-distance", "199.0", "--wavelength", "1.294", "--polarization", "0.998", "-C", "92.044,93.019,49.014,90,92.69,90", "-S", "P21"], "tiers": {}},
{"id": "lcls242_t", "cxidb": 242, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "9O4T", "sg": "P 1 21 1", "d_cut": 1.95, "r_free_deposited": 0.2348, "images_deposited": null, "inputs": ["lcls_242/xtc/*.xtc", "lcls_242/xtc_more/*.xtc"], "args": ["--detector-distance", "199.0", "--wavelength", "1.294", "--polarization", "0.998", "-C", "96.031,94.536,50.529,90,91.18,90", "-S", "P21"], "tiers": {}},
{"id": "euxfel83", "cxidb": 83, "facility": "European XFEL", "beamline": "SPB/SFX", "detector": "AGIPD 1M (200 um)", "format": "Cheetah CXI", "pdb": "6GTH", "sg": "P 32 2 1", "d_cut": 1.69, "r_free_deposited": 0.2096, "images_deposited": 14445, "inputs": ["euxfel_83/raw/*.cxi"], "args": ["--crystfel-geometry", "{data}/euxfel_83/ref/agipd_mar18_v10.geom", "--gain", "60", "--wavelength", "1.3332", "--refine-geometry=off", "-C", "41.84,41.84,233.28,90,90,120", "-S", "P3221"], "max_images": 2000, "tiers": {"smoke": {"images": 2000}}},
{"id": "euxfel152", "cxidb": 152, "facility": "European XFEL", "beamline": "SPB/SFX", "detector": "AGIPD 1M (200 um)", "format": "Cheetah CXI", "pdb": "6U57", "sg": "I 2 3", "d_cut": 2.8, "r_free_deposited": 0.2489, "images_deposited": 37006, "inputs": ["euxfel_152/raw/*.cxi"], "args": ["--crystfel-geometry", "{data}/euxfel_152/ref/kdo_embedded.geom", "--gain", "62", "--wavelength", "1.3332", "--refine-geometry=off", "-C", "118,118,118,90,90,90", "-S", "I23"], "max_images": 2000, "tiers": {"smoke": {"images": 2000}}},
{"id": "alvra103", "cxidb": 103, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 16M (75 um)", "format": "SwissFEL HDF5, float32 keV", "pdb": "6S0L", "sg": "C 2 2 21", "d_cut": 2.65, "r_free_deposited": 0.2203, "images_deposited": 199136, "inputs": ["swissfel_103/raw/run*.JF06T32V01.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_103/ref/jf-16M_mask.geom", "--gain", "4.57", "--wavelength", "2.7130", "-C", "40.34,180.66,143.05,90,90,90", "-S", "C2221"], "tiers": {}},
{"id": "alvra103_int16", "cxidb": 103, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 16M (75 um)", "format": "int16 photons, bitshuffle/LZ4 copy", "pdb": "6S0L", "sg": "C 2 2 21", "d_cut": 2.65, "r_free_deposited": 0.2203, "images_deposited": 199136, "inputs": ["swissfel_103/conv/run*_int16.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_103/ref/jf-16M_mask.geom", "--gain", "1", "--wavelength", "2.7130", "-C", "40.34,180.66,143.05,90,90,90", "-S", "C2221"], "tiers": {}},
{"id": "alvra213", "cxidb": 213, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 4M (75 um)", "format": "SwissFEL HDF5, float32 keV", "pdb": "8BKH", "sg": "P 1 21 1", "d_cut": 1.35, "r_free_deposited": 0.2271, "images_deposited": null, "inputs": ["swissfel_213/raw/march_dark_MbCO_II-March-06/data/dark/run_*.JF06T08V01.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_213/ref/mbco_march_mask.geom", "--gain", "12.037", "--wavelength", "1.0300", "-C", "64.1,28.8,35.8,90,106.9,90", "-S", "P21"], "tiers": {}},
{"id": "alvra213_int16", "cxidb": 213, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 4M (75 um)", "format": "int16 photons, bitshuffle/LZ4 copy", "pdb": "8BKH", "sg": "P 1 21 1", "d_cut": 1.35, "r_free_deposited": 0.2271, "images_deposited": null, "inputs": ["swissfel_213/conv/march_dark_MbCO_II-March-06/data/dark/run_*_int16.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_213/ref/mbco_march_mask.geom", "--gain", "1", "--wavelength", "1.0300", "-C", "64.1,28.8,35.8,90,106.9,90", "-S", "P21"], "tiers": {}}
{"id": "lcls222", "cxidb": 222, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "8TDQ", "sg": "P 65 2 2", "d_cut": 1.65, "r_free_deposited": 0.2012, "images_deposited": null, "inputs": ["lcls_222/xtc/*.xtc", "lcls_222/xtc_more/*.xtc"], "args": ["-C", "78.616,78.616,265.275,90,90,120", "-S", "P6522"], "tiers": {"smoke": {"images": 1500}}},
{"id": "lcls242_s", "cxidb": 242, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "9O4S", "sg": "P 1 21 1", "d_cut": 1.95, "r_free_deposited": 0.2102, "images_deposited": null, "inputs": ["lcls_242/xtc/*.xtc", "lcls_242/xtc_more/*.xtc"], "args": ["--wavelength", "1.294", "--polarization", "0.998", "-C", "92.044,93.019,49.014,90,92.69,90", "-S", "P21"], "tiers": {}},
{"id": "lcls242_t", "cxidb": 242, "facility": "LCLS", "beamline": "MFX", "detector": "Rayonix MX340-HS (4x4 binned, 177 um)", "format": "LCLS-I XTC", "pdb": "9O4T", "sg": "P 1 21 1", "d_cut": 1.95, "r_free_deposited": 0.2348, "images_deposited": null, "inputs": ["lcls_242/xtc/*.xtc", "lcls_242/xtc_more/*.xtc"], "args": ["--wavelength", "1.294", "--polarization", "0.998", "-C", "96.031,94.536,50.529,90,91.18,90", "-S", "P21"], "tiers": {}},
{"id": "euxfel83", "cxidb": 83, "facility": "European XFEL", "beamline": "SPB/SFX", "detector": "AGIPD 1M (200 um)", "format": "Cheetah CXI", "pdb": "6GTH", "sg": "P 32 2 1", "d_cut": 1.69, "r_free_deposited": 0.2096, "images_deposited": 14445, "inputs": ["euxfel_83/raw/*.cxi"], "args": ["--crystfel-geometry", "{data}/euxfel_83/ref/agipd_mar18_v10.geom", "--wavelength", "1.3332", "-C", "41.84,41.84,233.28,90,90,120", "-S", "P3221"], "max_images": 2000, "tiers": {"smoke": {"images": 2000}}},
{"id": "euxfel152", "cxidb": 152, "facility": "European XFEL", "beamline": "SPB/SFX", "detector": "AGIPD 1M (200 um)", "format": "Cheetah CXI", "pdb": "6U57", "sg": "I 2 3", "d_cut": 2.8, "r_free_deposited": 0.2489, "images_deposited": 37006, "inputs": ["euxfel_152/raw/*.cxi"], "args": ["--crystfel-geometry", "{data}/euxfel_152/ref/kdo_embedded.geom", "--gain", "62", "--wavelength", "1.3332", "-C", "118,118,118,90,90,90", "-S", "I23"], "max_images": 2000, "tiers": {"smoke": {"images": 2000}}},
{"id": "alvra103", "cxidb": 103, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 16M (75 um)", "format": "SwissFEL HDF5, float32 keV", "pdb": "6S0L", "sg": "C 2 2 21", "d_cut": 2.65, "r_free_deposited": 0.2203, "images_deposited": 199136, "inputs": ["swissfel_103/raw/run*.JF06T32V01.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_103/ref/jf-16M_mask.geom", "--wavelength", "2.7130", "-C", "40.34,180.66,143.05,90,90,90", "-S", "C2221"], "tiers": {}},
{"id": "alvra103_int16", "cxidb": 103, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 16M (75 um)", "format": "int16 photons, bitshuffle/LZ4 copy", "pdb": "6S0L", "sg": "C 2 2 21", "d_cut": 2.65, "r_free_deposited": 0.2203, "images_deposited": 199136, "inputs": ["swissfel_103/conv/run*_int16.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_103/ref/jf-16M_mask.geom", "--wavelength", "2.7130", "-C", "40.34,180.66,143.05,90,90,90", "-S", "C2221"], "tiers": {}},
{"id": "alvra213", "cxidb": 213, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 4M (75 um)", "format": "SwissFEL HDF5, float32 keV", "pdb": "8BKH", "sg": "P 1 21 1", "d_cut": 1.35, "r_free_deposited": 0.2271, "images_deposited": null, "inputs": ["swissfel_213/raw/march_dark_MbCO_II-March-06/data/dark/run_*.JF06T08V01.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_213/ref/mbco_march_mask.geom", "--wavelength", "1.0300", "-C", "64.1,28.8,35.8,90,106.9,90", "-S", "P21"], "tiers": {}},
{"id": "alvra213_int16", "cxidb": 213, "facility": "SwissFEL", "beamline": "Alvra", "detector": "JUNGFRAU 4M (75 um)", "format": "int16 photons, bitshuffle/LZ4 copy", "pdb": "8BKH", "sg": "P 1 21 1", "d_cut": 1.35, "r_free_deposited": 0.2271, "images_deposited": null, "inputs": ["swissfel_213/conv/march_dark_MbCO_II-March-06/data/dark/run_*_int16.h5"], "args": ["--crystfel-geometry", "{data}/swissfel_213/ref/mbco_march_mask.geom", "--wavelength", "1.0300", "-C", "64.1,28.8,35.8,90,106.9,90", "-S", "P21"], "tiers": {}}
]}