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Jungfraujoch/tools/battery/still_manifest.json
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leonarski_f 15793a6bc2 still battery: no --polarization on the two forms of the turned-plane LCLS run 
The plane is now taken from the background for the integration as well as the shadow mask, and the
degree (0.99 by default against the 0.998 passed) moves neither the mask nor R_free beyond 0.0001.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit ebf0f24351cf45c5e3d7aefeae1e5df83ff0fd55)
2026-10-23 17:56:51 +02:00

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{"_comment": "The still battery (still_battery.py). inputs: globs relative to the site's still data_root, each glob's matches sorted by name; {data} in args is the data root. Every set runs with its deposition's cell and space group (-C/-S); r_free_deposited is the entry's published R-free (dark/ground-state entries only); d_cut is the deposition's resolution. Where to get the data: docs/EXTERNAL_TEST_DATA_STILLS.md.",
"sets": [
{"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": ["-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": ["-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", "-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", "-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"], "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", "--wavelength", "1.3332", "-C", "118,118,118,90,90,90", "-S", "I23"], "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": {}}
]}
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