diff --git a/broker/gen/model/Rugnux_live_shell.h b/broker/gen/model/Rugnux_live_shell.h
index 370bb6a62..78a6c4af0 100644
--- a/broker/gen/model/Rugnux_live_shell.h
+++ b/broker/gen/model/Rugnux_live_shell.h
@@ -127,7 +127,7 @@ public:
     bool rSplitIsSet() const;
     void unsetR_split();
     /// <summary>
-    /// R-free of the placed model (as given, not refined) over the shell&#39;s free reflections
+    /// R-free of the placed model (as given, not refined) over the shell&#39;s free reflections. In &#x60;overall&#x60;, the R-free of the model the run ended with: the refined model&#39;s (&#x60;model.refinement.r_free&#x60;) where rugnux refined it, else the placed model&#39;s (&#x60;model.r_free&#x60;). 
     /// </summary>
     double getRFree() const;
     void setRFree(double const value);
diff --git a/broker/gen/model/Rugnux_live_status.h b/broker/gen/model/Rugnux_live_status.h
index 06f4edded..c1c53a2db 100644
--- a/broker/gen/model/Rugnux_live_status.h
+++ b/broker/gen/model/Rugnux_live_status.h
@@ -113,7 +113,7 @@ public:
     bool shellsMergeIsSet() const;
     void unsetShells_merge();
     /// <summary>
-    /// Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of &#x60;_report.txt&#x60;. Rotation: once the run is over; serial: at each provisional merge and at the end. &#x60;overall&#x60; is the same table&#39;s \&quot;Overall\&quot; row (whole-merge completeness, multiplicity, I/sigma, CC1/2, R_meas or R_split, CCref, and the overall R-free of the model validated on it), present with &#x60;shells&#x60;. 
+    /// Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of &#x60;_report.txt&#x60;. Rotation: once the run is over; serial: at each provisional merge and at the end. &#x60;overall&#x60; is the same table&#39;s \&quot;Overall\&quot; row (whole-merge completeness, multiplicity, I/sigma, CC1/2, R_meas or R_split, CCref, and the R-free of the final model - refined where rugnux refined it, as &#x60;model.refinement.r_free&#x60;, else as placed, as &#x60;model.r_free&#x60;), present with &#x60;shells&#x60;. 
     /// </summary>
     std::vector<org::openapitools::server::model::Rugnux_live_shell> getShells() const;
     void setShells(std::vector<org::openapitools::server::model::Rugnux_live_shell> const& value);
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index 2a2237417..269fad3f8 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -3227,7 +3227,10 @@ components:
         r_free:
           type: number
           format: double
-          description: R-free of the placed model (as given, not refined) over the shell's free reflections
+          description: |
+            R-free of the placed model (as given, not refined) over the shell's free reflections. In `overall`, the
+            R-free of the model the run ended with: the refined model's (`model.refinement.r_free`) where rugnux
+            refined it, else the placed model's (`model.r_free`).
     rugnux_live_frame_range:
       type: object
       description: |
@@ -3313,7 +3316,8 @@ components:
             Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of
             `_report.txt`. Rotation: once the run is over; serial: at each provisional merge and at the end.
             `overall` is the same table's "Overall" row (whole-merge completeness, multiplicity, I/sigma, CC1/2,
-            R_meas or R_split, CCref, and the overall R-free of the model validated on it), present with `shells`.
+            R_meas or R_split, CCref, and the R-free of the final model - refined where rugnux refined it, as
+            `model.refinement.r_free`, else as placed, as `model.r_free`), present with `shells`.
           items:
             $ref: '#/components/schemas/rugnux_live_shell'
         overall:
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index d7da8212d..c5b40f102 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -553,7 +553,9 @@ If parameter is not provided calibration will be saved only if more than 4 image
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="smargon"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand smargon"><span class="property-name">smargon</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">object</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Geometry of Smargon goniometer at SLS 2.0 / MX beamlines. 
 Assuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="max_spot_count"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">max_spot_count</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">integer</span><span> <span class="sc-Nxspf sc-fxwrCY cXxAXt eMVOei"> <!-- -->[ 10 .. 2000 ]<!-- --> </span></span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">250</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected</p>
-</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="detect_ice_rings"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">detect_ice_rings</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">boolean</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Flag spots as ice rings and reduce their effect on indexing</p>
+</div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="detect_ice_rings"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">detect_ice_rings</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">boolean</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Flag spots as ice rings and reduce their effect on indexing. Left out, the broker&#39;s own
+spot finding treats no spot as an ice ring, rugnux live decides as a bare <code>rugnux</code> would (on
+for a rotation sweep, off for stills), and the master file carries no <code>detect_ice_rings</code>.</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="async_start"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">async_start</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">boolean</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">false</span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>When set to true, <code>/start</code> will not wait for detector and Jungfraujoch to be ready for the measurement.</p>
 </div></div></div></td></tr><tr class=""><td class="sc-dLMFU sc-eldPxv sc-hCPjZK hZbWKe jXkfaY GCgeS" kind="field" title="module_placement"><span class="sc-gFqAkR eRqgPI"></span><button aria-label="expand module_placement"><span class="property-name">module_placement</span><svg class="sc-cwHptR ivsSRP" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR">Array of </span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">objects</span><span class="sc-Nxspf sc-gmPhUn cXxAXt hjnRRA"> (<!-- -->detector_module_placement<!-- -->) </span></div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Where the detector&#39;s modules lie for this dataset, as rugnux measures them: rugnux writes
 <code>&lt;prefix&gt;_module_placement.json</code>, which holds exactly this field, to be merged into the dataset settings.
@@ -1144,7 +1146,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
-      const __redoc_state = {"menu":{"activeItemIdx":-1},"spec":{"data":{"openapi":"3.0.3","info":{"title":"Jungfraujoch","description":"API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).\nJungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.\nJungfraujoch uses FPGA boards to acquire data at high data rates.\n\n# License Clarification\n\nWhile this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**\nwhen this file is used solely to generate OpenAPI clients or when implementing applications that\ninteract with the API. Generated client code and applications using this API definition are not\nsubject to the GPL license requirements and may be distributed under terms of your choosing.\n\nThis exception is similar in spirit to the Linux Kernel's approach to userspace API headers and\nthe GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.186","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"securitySchemes":{"bearerAuth":{"type":"http","scheme":"bearer","description":"Per-dataset secret. `/start` may carry one or more equivalent `tokens`; while the current\ndataset has any, the operations marked with this scheme require `Authorization: Bearer <token>`\nand answer 401 otherwise. A dataset started without `tokens` is not protected and the header is ignored.\n"}},"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","spindle_blind_fraction","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","compression_ratio","ice_ring_score"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"},"saturation":{"in":"query","name":"saturation","required":false,"schema":{"type":"number","format":"float","minimum":-32767,"maximum":32767},"description":"Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"},"background":{"in":"query","name":"background","required":false,"schema":{"type":"number","format":"float","default":0,"minimum":-32767,"maximum":32767},"description":"Background value to set contrast in the preview image"},"show_spots":{"in":"query","name":"show_spots","schema":{"type":"boolean","default":true},"description":"Show spot finding results on the image"},"show_predictions":{"in":"query","name":"show_predictions","schema":{"type":"boolean","default":false},"description":"Show Bragg spot predictions on the image (if available for the image)"},"show_beam_center":{"in":"query","name":"show_beam_center","schema":{"type":"boolean","default":true},"description":"Show beam center on the image"},"show_roi":{"in":"query","name":"show_roi","schema":{"type":"boolean","default":false},"description":"Show ROI areas on the image"},"jpeg_quality":{"in":"query","name":"jpeg_quality","description":"Quality of JPEG image (100 - highest; 0 - lowest)","schema":{"type":"integer","format":"int64","default":100,"minimum":0,"maximum":100}},"show_user_mask":{"in":"query","name":"show_user_mask","schema":{"type":"boolean","default":false},"description":"Show user mask"},"resolution_ring":{"in":"query","name":"show_res_ring","description":"Show resolution ring, provided in Angstrom","schema":{"type":"number","format":"float","default":0.1,"minimum":0.1,"maximum":100}},"resolution_estimate":{"in":"query","name":"show_res_est","description":"Show resolution estimation as a ring","schema":{"type":"boolean","default":false}},"color_scale":{"in":"query","name":"color","description":"Color scale for preview image","schema":{"type":"string","enum":["indigo","viridis","bw","wb","green","heat","magma","inferno"],"default":"indigo"}}},"schemas":{"grid_scan":{"description":"Definition of a grid scan. Combine it with a goniometer axis to state the angle the spindle\nstood at: send `goniometer` with `step` 0 and the `start` angle of the grid scan, and that\nangle is written per image into the NXmx sample transformation chain. Without one the\nspindle is recorded at 0, which says that nobody stated an angle rather than that the\nspindle stood at 0.\n","type":"object","required":["n_fast","step_x_um","step_y_um"],"properties":{"n_fast":{"type":"integer","format":"int64","minimum":1,"example":20,"description":"Number of elements in the fast direction"},"step_x_um":{"type":"number","format":"float","example":5,"description":"Step in grid along the fast direction. Can be negative. \nPositive number: left to right\nNegative number: right to left\n"},"step_y_um":{"type":"number","format":"float","example":-3,"description":"Step in grid along the slow direction. Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees. 0 for an axis that does not turn: the axis then\nrecords the angle the spindle stood at, which is how a grid scan or a set of stills\nstates its head position.\n"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\nFlex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).\n","enum":["BeamCenter","OrientationOnly","Flex","None"]},"integration_model":{"type":"string","description":"Bragg spot integration model.\nProfileGaussian - profile fit with a measured-width Gaussian (Kabsch-style), the default; more\n  accurate intensities than box summation.\nProfileEmpirical - profile fit with a per-resolution-shell empirical profile learned from strong spots.\nBoxSum - classical uniform box summation minus a ring-mean background; the simpler, faster fallback.\n","enum":["ProfileGaussian","ProfileEmpirical","BoxSum"],"default":"ProfileGaussian"},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. If left empty, no file will be saved."},"images_per_file":{"type":"integer","format":"int64","minimum":1,"description":"Number of images in a single HDF5 data file, taken literally when given.\nIf omitted, it is chosen from the acquisition: a rotation sweep of at most 20000 images\ngoes into a single data file, so the dataset stays readable by programs that follow only\nthe first data file of a legacy master; a grid scan is split on a whole number of fast-axis\nrows; anything else (stills, serial) uses 1000.\n"},"space_group_number":{"type":"integer","format":"int64","minimum":1,"maximum":230,"description":"Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","bszstd_rlehuf","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","minimum":0,"description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"beam_size_x_um":{"type":"number","format":"float","minimum":0,"description":"First element of /entry/instrument/beam/incident_beam_size in NXmx\nHorizontal size of the X-ray beam where it meets the sample - the FWHM of a focused beam,\nthe full width of a slit-defined one. [um]\n"},"beam_size_y_um":{"type":"number","format":"float","minimum":0,"description":"Second element of /entry/instrument/beam/incident_beam_size in NXmx\nVertical size of the X-ray beam where it meets the sample. [um]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments\nand to turn off for other experiments.\n"},"save_calibration":{"type":"boolean","description":"Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.\nIf parameter is not provided calibration will be saved only if more than 4 images are recorded.\n"},"polarization_factor":{"type":"number","description":"Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization","format":"float","minimum":-1,"maximum":1},"ring_current_mA":{"type":"number","format":"float","description":"Ring current at the beginning of the data collection","minimum":0},"sample_temperature_K":{"type":"number","format":"float","description":"Sample temperature in Kelvin","minimum":0},"poni_rot1_rad":{"type":"number","description":"PONI angle rot1 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot2_rad":{"type":"number","description":"PONI angle rot2 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot3_rad":{"type":"number","description":"PONI angle rot3 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"unit_cell":{"$ref":"#/components/schemas/unit_cell"},"spot_finding":{"type":"boolean","description":"Enable spot finding and save spots","default":true},"smargon":{"type":"object","description":"Geometry of Smargon goniometer at SLS 2.0 / MX beamlines. \nAssuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.\n","required":["phi_deg","chi_deg"],"properties":{"phi_deg":{"type":"number","format":"float","description":"Phi angle in degrees"},"chi_deg":{"type":"number","format":"float","description":"Chi angle in degrees"},"phi_axis":{"type":"array","description":"Phi rotation axis","default":[1,0,0],"example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"chi_axis":{"type":"array","description":"Chi rotation axis","default":[0,0,1],"example":[0,0,1],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3}}},"max_spot_count":{"type":"integer","minimum":10,"maximum":2000,"default":250,"description":"Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected"},"detect_ice_rings":{"type":"boolean","description":"Flag spots as ice rings and reduce their effect on indexing"},"async_start":{"type":"boolean","default":false,"description":"When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement."},"module_placement":{"type":"array","items":{"$ref":"#/components/schemas/detector_module_placement"},"description":"Where the detector's modules lie for this dataset, as rugnux measures them: rugnux writes\n`<prefix>_module_placement.json`, which holds exactly this field, to be merged into the dataset settings.\nEach entry names its module by its readout pixel 0 and readout axes in the stored image (`x0`, `y0`,\n`fast_axis`, `slow_axis`, after `mirror_y`; see `detector_module_placement`), in any order; every\nmodule must be named once, and only modules of the detector, else `/start` fails with 400. The image\nis assembled as configured (`custom_geometry`); the placement goes into the start message and the\nNXmx `module_NN` groups, and the analysis takes it. Omitted or empty:\nmodules as assembled.\n"},"tokens":{"type":"array","items":{"type":"string","minLength":1},"writeOnly":true,"description":"Bearer tokens that protect this dataset: any number, all equivalent (e.g. a beamline\nsecret and a dataset-specific user secret). While set, the endpoints marked with the\n`bearerAuth` security scheme require `Authorization: Bearer <token>` and answer 401 otherwise.\nEvery accepted `/start` replaces the previous dataset's tokens; omitted or empty means no\nprotection. Never returned by any endpoint.\n"},"xray_fluorescence_spectrum":{"type":"object","required":["energy_eV","data"],"properties":{"energy_eV":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan energy for each measurement point"},"data":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV"}}}}},"crystal_lattice":{"type":"array","items":{"type":"number","format":"float"},"minItems":9,"maxItems":9,"description":"Real-space crystal lattice 3D vectors in Angstrom.\nOrder is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)\n"},"unit_cell":{"type":"object","description":"Unit cell parameters. Necessary to run indexing. Units of angstrom and degree","required":["a","b","c","alpha","beta","gamma"],"properties":{"a":{"type":"number","format":"float","example":37,"minimum":0},"b":{"type":"number","format":"float","example":37,"minimum":0},"c":{"type":"number","format":"float","example":78,"minimum":0},"alpha":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"beta":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"gamma":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360}}},"file_writer_format":{"type":"string","enum":["NXmxOnlyData","NXmxLegacy","NXmxVDS","NXmxIntegrated","CBF","TIFF","NoFileWritten"],"default":"NXmxVDS","description":"NoFileWritten - no files are written at all\nNXmxOnlyData - only data files are written, no master file\nNXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia\nNXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling\nNXmxIntegrated - single HDF5 per dataset\nCBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\nTIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\n"},"file_writer_settings":{"type":"object","properties":{"overwrite":{"type":"boolean","default":false,"description":"Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.\n"},"format":{"$ref":"#/components/schemas/file_writer_format"}}},"pixel_mask_statistics":{"type":"object","properties":{"user_mask":{"description":"Number of pixels masked using the user mask","type":"integer","format":"int64","minimum":0},"too_high_pedestal_rms":{"description":"Number of pixels with G0 pedestal RMS higher than provided threshold","type":"integer","format":"int64","minimum":0},"wrong_gain":{"description":"Number of pixels that show wrong gain level during the pedestal procedure","type":"integer","format":"int64","minimum":0}}},"image_buffer_status":{"type":"object","required":["image_numbers","total_slots","in_preparation_slots","in_sending_slots","available_slots","max_image_number","min_image_number"],"properties":{"min_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Smallest image number available in the buffer"},"max_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Largest image number available in the buffer"},"image_numbers":{"type":"array","description":"Image numbers currently present in the buffer.","items":{"type":"integer","format":"int64"}},"total_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer. This number, compared to number of images in data collection and\nframe rate will determine \"retention\" rate of the image buffer.\n"},"available_slots":{"type":"integer","format":"int64","description":"Slots available for the data collection"},"in_preparation_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently in preparation for sending.\n"},"in_sending_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently sending/writing data.\n"},"current_counter":{"type":"integer","format":"int64","description":"Counter of changes in the image buffer - either new start message or new image added.\nFor optimization one can only load new images/datasets from the HTTP if this value changes.\nCounter is optional as it was not implemented in older versions to avoid breaking change\n"}}},"image_format_settings":{"type":"object","required":["summation","jungfrau_conversion","geometry_transform","mask_chip_edges","mask_module_edges","apply_mask"],"properties":{"summation":{"type":"boolean","description":"Enable summation of images to a given image_time\nIf disabled images are saved according to original detector speed, but image count is adjusted\n"},"geometry_transform":{"type":"boolean","description":"Place module read-out into their location on composed detector and extend multipixels\n"},"jungfrau_conversion":{"type":"boolean","description":"Convert pixel value in ADU to photon counts/energy\nOnly affects JUNGFRAU detector\n"},"jungfrau_conversion_factor_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to convert energy deposited into pixel to counts\nIf not provided incident_energy_keV is used\n"},"bit_depth_image":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of resulting image (it doesn't affect the detector read-out value)\nIf not provided value is adjusted automatically\n"},"signed_output":{"type":"boolean","description":"Controls if pixels have signed output\nIf not provided value is adjusted automatically\n"},"mask_module_edges":{"type":"boolean","default":true,"description":"Mask 1 pixel on the module boundary\n"},"mask_chip_edges":{"type":"boolean","default":true,"description":"Mask multipixels on chip boundary\n"},"jungfrau_mask_pixels_without_g0":{"type":"boolean","default":true,"description":"JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.\nThis should be turned off for cases, where detector is operated at room temperature with long exposure time.\n"},"apply_mask":{"type":"boolean","default":false,"description":"Masked pixels are set to special value in the images produced by Jungfraujoch\n"},"jungfrau_pedestal_g0_rms_limit":{"type":"integer","format":"int64","default":100,"minimum":0,"description":"Pixels with pedestal G0 RMS above the threshold are marked as masked pixels"}}},"detector_power_state":{"type":"string","description":"Power on of ASICs","enum":["PowerOn","PowerOff","Partial"]},"detector_state":{"type":"string","description":"Current state of the detector","enum":["Idle","Waiting","Busy","Error","Not connected"]},"detector_status":{"type":"object","required":["state","powerchip","server_version","number_of_triggers_left","fpga_temp_degC","high_voltage_V"],"properties":{"state":{"$ref":"#/components/schemas/detector_state"},"powerchip":{"$ref":"#/components/schemas/detector_power_state"},"server_version":{"type":"string","description":"Detector server (on read-out boards) version"},"number_of_triggers_left":{"type":"integer","format":"int64","description":"Remaining triggers to the detector (max of all modules)"},"fpga_temp_degC":{"type":"array","description":"Temperature of detector FPGAs","items":{"type":"integer","format":"int64"}},"high_voltage_V":{"type":"array","description":"High voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real detector"},"internal_frame_generator_images":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":64,"description":"Number of images stored in the internal frame generator."},"detector_trigger_delay_ns":{"type":"integer","format":"int64","minimum":0,"default":0,"description":"Delay between TTL trigger and acquisition start [ns]"},"timing":{"$ref":"#/components/schemas/detector_timing"},"eiger_threshold_keV":{"type":"number","format":"float","minimum":1,"maximum":100,"description":"Threshold for the PSI EIGER detector and all DECTRIS detectors.\nIf value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.\nIf value is not provided, threshold will be determined on start of acquisition as half of incident energy. \nThis might lead to increased start time.\n"},"eiger_bit_depth":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of PSI EIGER read-out. This is  \nIf value is not provided, depth will be determined based on the image time:\n* Exposure time < 500 microseconds depth of 8 bit will be used,\n* 500 <= exposure time < 2622 microseconds depth of 16 bit will be used\n* Exposure time >= 2622 microseconds depth of 32 bit will be used.\n"},"jungfrau_pedestal_g0_frames":{"type":"integer","format":"int64","default":2000,"minimum":0},"jungfrau_pedestal_g1_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_g2_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_min_image_count":{"type":"integer","format":"int64","default":128,"minimum":32,"description":"Minimum number of collected images for pedestal to consider it viable"},"jungfrau_storage_cell_count":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":16},"jungfrau_storage_cell_delay_ns":{"type":"integer","format":"int64","minimum":2100,"default":5000,"description":"Delay between two storage cells [ns]"},"jungfrau_fixed_gain_g1":{"type":"boolean","default":false,"description":"Fix gain to G1 (can be useful for storage cells)"},"jungfrau_use_gain_hg0":{"type":"boolean","default":false,"description":"Use high G0 (for low energy applications)"}}},"spot_finding_settings":{"type":"object","required":["enable","indexing","signal_to_noise_threshold","photon_count_threshold","max_pix_per_spot","min_pix_per_spot","high_resolution_limit_for_spot_count_low_res","ice_ring_width_q_recipA"],"properties":{"enable":{"type":"boolean","default":true,"description":"Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. \nEven if disabled spot finding information will still be send and written, though always with zero spots.\n"},"indexing":{"type":"boolean","default":true,"description":"Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.\n"},"signal_to_noise_threshold":{"type":"number","format":"float","minimum":0},"photon_count_threshold":{"type":"integer","format":"int64","minimum":0},"min_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"max_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"high_resolution_limit":{"type":"number","format":"float","description":"High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends\nas far as the detector reaches, i.e. the detection is not clipped in resolution.\n"},"low_resolution_limit":{"type":"number","format":"float","description":"Low resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding is not\nclipped at the low-resolution end. A value of 0 is accepted and means the same thing.\n"},"high_resolution_limit_for_spot_count_low_res":{"type":"number","format":"float","description":"High resolution threshold to consider spot \"low resolution\" [Angstrom]","minimum":2,"maximum":8},"quick_integration":{"type":"boolean","default":false,"deprecated":true,"description":"Ignored: accepted on input and always returned as false; will be removed in a future release.\nThe Lite and FPGA workflows index images but do not integrate them; integration is done by rugnux live.\n"},"ice_ring_width_q_recipA":{"type":"number","format":"float","minimum":0,"maximum":1,"default":0.03,"description":"Half-width of the ice ring band in q (1/A). Matches the offline default in image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online."},"high_res_gap_Q_recipA":{"type":"number","format":"float","minimum":0.1,"maximum":5,"default":1.5,"description":"This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.\nIf there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.\nThis option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.\n"},"adaptive_threshold":{"type":"boolean","default":false,"description":"Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring\nthreshold derived from each image's own noise, so the same setting works across datasets without\nper-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the\noperating point instead.\nUsed only on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).\nThe JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold;\nthere the setting is accepted and ignored, so the same settings can be shared across detectors.\n"},"false_pixels_per_frame":{"type":"number","format":"float","minimum":1,"maximum":100000,"default":100,"description":"Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.\nAbout 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.\n"}}},"azim_int_settings":{"type":"object","required":["solid_angle_corr","polarization_corr","low_q_recipA"],"properties":{"polarization_corr":{"type":"boolean","description":"Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)","default":true},"solid_angle_corr":{"type":"boolean","description":"Apply solid angle correction for azimuthal integration","default":true},"high_q_recipA":{"type":"number","minimum":0.00002,"maximum":10,"format":"float","description":"Upper q limit of the azimuthal integration [1/Angstrom]. Optional: if omitted, the integration\n(and the adaptive spot detection that shares these q bins) extends to the highest q the\ndetector reaches.\n"},"low_q_recipA":{"type":"number","format":"float","minimum":0.00001,"maximum":10},"q_spacing":{"type":"number","format":"float","minimum":0.00001,"description":"Width of a Q bin [1/Angstrom], for linear binning only. Linear binning takes either this or\n`q_bins`, not both; with neither, the spacing is 0.01 1/Angstrom.\n"},"q_bins":{"type":"integer","format":"int64","minimum":1,"maximum":65534,"description":"Number of Q bins between low and high Q. Required for `log10` binning; for `linear` binning\nan alternative to `q_spacing`.\n"},"q_binning":{"$ref":"#/components/schemas/q_binning"},"azimuthal_bins":{"type":"integer","format":"int64","minimum":1,"maximum":512,"default":1,"description":"Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration"},"force_cpu":{"type":"boolean","default":false,"description":"Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.\nThis allows to extend number of azimuthal integration bins, as well as to calculate standard deviation\nof the azimuthal integration results.\n"}}},"q_binning":{"type":"string","description":"How the Q bins of azimuthal integration are laid out between low and high Q.\nlinear - equal steps in Q.\nlog10 - equal steps in log10(Q): fine bins at low Q, coarse at high Q. Needs `q_bins`.\n","enum":["linear","log10"],"default":"linear"},"detector_list_element":{"type":"object","required":["id","nmodules","description","width","height","serial_number","base_ipv4_addr","udp_interface_count","readout_time_ns","min_frame_time_ns","min_count_time_ns"],"properties":{"id":{"type":"integer","format":"int64","minimum":0},"description":{"type":"string","example":"JUNGFRAU 4 Mpixel"},"serial_number":{"type":"string","example":"JF17T16V01"},"base_ipv4_addr":{"type":"string","example":"10.10.10.1"},"udp_interface_count":{"type":"integer","format":"int64","example":2,"description":"Number of UDP interfaces per detector module"},"nmodules":{"type":"integer","format":"int64","example":18},"width":{"type":"integer","format":"int64","example":2068},"height":{"type":"integer","format":"int64","example":2164},"pixel_size_mm":{"type":"number","format":"float","example":0.075},"readout_time_ns":{"type":"integer","format":"int64"},"min_frame_time_ns":{"type":"integer","format":"int64"},"min_count_time_ns":{"type":"integer","format":"int64"},"type":{"$ref":"#/components/schemas/detector_type"}}},"detector_list":{"type":"object","required":["detectors","current_id"],"properties":{"detectors":{"type":"array","items":{"$ref":"#/components/schemas/detector_list_element"}},"current_id":{"type":"integer","format":"int64","example":0}}},"detector_selection":{"type":"object","required":["id"],"properties":{"id":{"type":"integer","format":"int64","example":1}}},"measurement_statistics":{"type":"object","properties":{"file_prefix":{"type":"string"},"run_number":{"type":"integer","format":"int64","description":"Number of data collection run. This can be either automatically incremented or provided externally for each data collection.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number).\n"},"images_expected":{"type":"integer","format":"int64"},"images_collected":{"type":"integer","format":"int64","description":"Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.\n"},"images_sent":{"type":"integer","format":"int64","description":"Images sent to the writer. \nThe value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.\n"},"images_written":{"type":"integer","format":"int64","description":"Images successfully written to disk.\nThe value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.\n"},"images_discarded_lossy_compression":{"type":"integer","format":"int64","description":"Images discarded by the lossy compression filter"},"max_image_number_sent":{"type":"integer","format":"int64"},"collection_efficiency":{"type":"number","format":"float","example":1,"minimum":0,"maximum":1},"compression_ratio":{"type":"number","format":"float","example":5.3,"minimum":0},"cancelled":{"type":"boolean"},"max_receiver_delay":{"type":"integer","format":"int64"},"indexing_rate":{"type":"number","format":"float"},"detector_width":{"type":"integer","format":"int64"},"detector_height":{"type":"integer","format":"int64"},"detector_pixel_depth":{"type":"integer","format":"int64","enum":[2,4]},"bkg_estimate":{"type":"number","format":"float"},"unit_cell":{"type":"string"},"error_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of error pixels on the detector"},"saturated_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of saturated pixels on the detector"},"roi_beam_pixels":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor number of valid pixels within this ROI\n"},"roi_beam_sum":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor sum of valid pixels within this ROI\n"}}},"fpga_status":{"type":"array","items":{"type":"object","required":["pci_dev_id","serial_number","base_mac_addr","eth_link_status","eth_link_count","eth_link_speed","power_usage_W","fpga_temp_C","hbm_temp_C","packets_sls","packets_udp","idle","fw_version","pcie_link_speed","pcie_link_width"],"properties":{"pci_dev_id":{"type":"string"},"serial_number":{"type":"string"},"fw_version":{"type":"string"},"base_mac_addr":{"type":"string"},"eth_link_count":{"type":"integer","format":"int64"},"eth_link_status":{"type":"integer","format":"int64"},"power_usage_W":{"type":"number","format":"float"},"fpga_temp_C":{"type":"number","format":"float"},"hbm_temp_C":{"type":"number","format":"float"},"packets_udp":{"type":"integer","format":"int64"},"packets_sls":{"type":"integer","format":"int64"},"idle":{"type":"boolean"},"pcie_link_speed":{"type":"integer","format":"int64","description":"PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)"},"pcie_link_width":{"type":"integer","format":"int64","description":"PCIe link width (expected value is 8 == x8)"}}}},"broker_status":{"type":"object","required":["state"],"properties":{"state":{"type":"string","enum":["Inactive","Idle","Busy","Measuring","Pedestal","Error"]},"progress":{"type":"number","format":"float","description":"Progress of data collection (only available if receiving is running)","example":1,"minimum":0,"maximum":1},"message":{"type":"string","description":"Message to display besides state of the jfjoch_broker; mostly used for errors and warnings\nThis matters especially for async functions (start/initialize), where API won't return reason\nfor the error during async operation.\n"},"message_severity":{"type":"string","enum":["success","info","warning","error"],"default":"error","description":"Level of the message to display"},"gpu_count":{"type":"integer","format":"int32","description":"Number of installed GPUs"},"broker_version":{"type":"string","description":"Version of the jfjoch_broker","example":"1.0.0-rc.128"}}},"image_pusher_status":{"type":"object","required":["pusher_type","addr","connected_writers"],"description":"Informs about status of the image pusher.\n","properties":{"pusher_type":{"$ref":"#/components/schemas/image_pusher_type"},"addr":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"List of addresses of image pushers.\nFor HDF5 socket - no addresses will be returned.\nFor ZeroMQ - list of addresses for each socket will be provided.\nFor TCP/IP - single address to connect all writers will be provided.\n"},"connected_writers":{"type":"integer","format":"int64","minimum":0,"description":"Number of connected writers \nFor ZeroMQ image socket: number is constant\nFor TCP/IP image socket: number is updated live during operation\n"},"images_written":{"type":"integer","format":"int64","minimum":0,"description":"Number of images written to the image socket.\nThis number is updated live during operation for TCP/IP image socket and direct HDF5 writer.\nIt is updated at the end of experiment for ZeroMQ image socket.\n"},"images_write_error":{"type":"integer","format":"int64","minimum":0,"description":"Number of images that could not be written to the image socket.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"},"writer_fifo_utilization":{"type":"array","items":{"type":"integer","format":"int64","minimum":0},"description":"Utilization of internal writer FIFO.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"}}},"plot":{"type":"object","required":["x","y","title"],"description":"x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly","properties":{"title":{"type":"string","default":""},"x":{"type":"array","items":{"type":"number","format":"float"}},"y":{"type":"array","items":{"type":"number","format":"float","nullable":true}},"z":{"type":"array","items":{"type":"number","format":"float","nullable":true}}}},"plot_unit_x":{"type":"string","enum":["image_number","q_recipA","d_A","angle_deg","ADU","grid_um"],"default":"image_number"},"plots":{"type":"object","required":["plot","unit_x"],"properties":{"title":{"type":"string"},"unit_x":{"$ref":"#/components/schemas/plot_unit_x"},"size_x":{"type":"number","format":"float","description":"Max X range of the plot"},"size_y":{"type":"number","format":"float","description":"Max Y range of the plot"},"plot":{"type":"array","items":{"$ref":"#/components/schemas/plot"}}}},"scan_result":{"type":"object","description":"Results of a scan","required":["images"],"properties":{"file_prefix":{"type":"string"},"rotation_unit_cell":{"$ref":"#/components/schemas/unit_cell"},"rotation_crystal_lattice":{"$ref":"#/components/schemas/crystal_lattice"},"rotation_bravais":{"type":"string","description":"Bravais lattice type of the global rotation-indexing solution: crystal-system\nletter + centering, e.g. \"tP\", \"oC\", \"cF\", \"hR\", \"mP\". Empty if not determined.\n"},"images":{"type":"array","items":{"type":"object","required":["efficiency","number"],"properties":{"efficiency":{"type":"number","format":"float"},"number":{"type":"integer","format":"int64","description":"Detector image number for a given cell"},"nx":{"type":"integer","format":"int64","description":"Cell position in X for grid scan"},"ny":{"type":"integer","format":"int64","description":"Cell position in Y for grid scan"},"angle":{"type":"number","format":"float","description":"Rotation angle associated with the image"},"bkg":{"type":"number","format":"float","description":"Background estimate"},"spindle_blind":{"type":"number","format":"float","description":"Fraction (0-1) of a rotation sweep's blind double cone that this orientation makes unrecoverable, assuming the nearest plausible lattice row is a lone 2-fold (a worst-case bound, not an estimate). At 0.5 and above a recovery protocol (second sweep, reorientation) should engage. Absent means the frame could not be assessed, which automation must treat the same as above threshold - it is not a zero.\n"},"spots":{"type":"integer","format":"int64","description":"Spot count"},"spots_low_res":{"type":"integer","format":"int64","description":"Spot count in low resolution range"},"spots_indexed":{"type":"integer","format":"int64","description":"Spot count within indexing tolerance"},"spots_ice":{"type":"integer","format":"int64","description":"Spot count within common ice ring resolutions"},"ice":{"type":"number","format":"float","description":"Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice)"},"index":{"type":"integer","format":"int64","description":"Indexing solution"},"latt_count":{"type":"integer","format":"int64","description":"Indexing lattice count"},"pr":{"type":"number","format":"float","description":"Profile radius, i.e. how far reflections are from the Ewald sphere"},"b":{"type":"number","format":"float","description":"B-Factor estimate"},"uc":{"$ref":"#/components/schemas/unit_cell"},"xfel_pulseid":{"type":"integer","format":"int64","description":"XFEL pulse ID"},"pixel_sum":{"type":"integer","format":"int64","description":"Total sum of all pixels"},"max":{"type":"integer","format":"int64","description":"Max viable pixel"},"sat":{"type":"integer","format":"int64","description":"Number of saturated pixels"},"err":{"type":"integer","format":"int64","description":"Number of error pixels"},"res":{"type":"number","format":"float","description":"Diffraction resolution estimate"}}}}}},"powder_calibration_fit_sigma":{"type":"object","description":"What the powder ring fit knows about its own answer, from the covariance of the converged\nproblem. Each sigma is in its parameter's own unit and is scaled by the residual scatter of\nthat fit, so it is the usual \"how far could this move before the fit got visibly worse\".\nThe two correlations are the ones that matter: a tilt and a beam-centre shift both displace a\nring's radius as cos(phi) and are told apart only by how that amplitude grows with the ring's\nradius, so as the rings run out the pair stops being separable and these approach 1.\nThe rotation sigmas and the correlations are absent when the tilt was not a free parameter.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI x [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI y [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Standard error of the fitted detector distance [mm]"},"poni_rot1_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot1 [rad]"},"poni_rot2_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot2 [rad]"},"correlation_beam_x_rot1":{"type":"number","format":"float","description":"Correlation between the fitted PONI x and rot1, -1 to 1"},"correlation_beam_y_rot2":{"type":"number","format":"float","description":"Correlation between the fitted PONI y and rot2, -1 to 1"}}},"powder_calibration_spot_check":{"type":"object","description":"Where the circle through the found spots puts the beam, and how far that is from the geometry\nactually fitted. An independent cross-check: it reads nothing from the file's own geometry, so\nit holds where the summed azimuthal profile does not - a profile binned about a badly wrong\ncentre shows each ring smeared across its sectors, and a fit on it converges on the wrong\nanswer without saying so. Two methods sharing no assumption, so the disagreement is the\nstatement. Absent when no spots were available.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Beam centre x the spots vote for [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Beam centre y the spots vote for [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Detector distance the spots imply [mm]"},"disagreement_pxl":{"type":"number","format":"float","description":"Distance between the spots' beam centre and the fitted one [pixels]"}}},"powder_calibration_quality":{"type":"object","description":"What a powder calibration knows about the geometry it produced. A calibration that has gone\nwrong - the wrong standard named, a header too far out for the rings to be found - looks\nexactly like one that has not until these are read.\n","properties":{"converged":{"type":"boolean","description":"Whether the geometry beside this is a measurement of the data at all. False means at least\none of its parameters was carried over from the input file rather than fitted - which looks\nexactly like a good fit in every other field here - and see not_converged_reason for which.\nrugnux --mode calibration writes no .poni file in that case, a PONI file having no field in\nwhich to say it, and exits non-zero.\n"},"not_converged_reason":{"type":"string","description":"What made converged false, in words. Absent when the calibration converged."},"calibrant":{"type":"string","description":"The powder standard the rings were fitted to, or the unit cell given in its place"},"method":{"type":"string","description":"How the rings were measured. rings fits the arcs of the run-summed (q x azimuth) azimuthal\nprofile; spots fits the pooled per-image spot lists.\n","enum":["rings","spots"]},"ring_points":{"type":"integer","format":"int64","description":"Ring measurements the fit used"},"rms_radial_pxl":{"type":"number","format":"float","description":"Scatter of those measurements about the fitted rings, as a radial distance [pixels]. The\nsingle number that separates a calibration that worked from one that did not.\n"},"beam_sigma_pxl":{"type":"number","format":"float","description":"Standard error the scatter implies on the beam centre [pixels], for a ring of that many\npoints. See powder_calibration_fit_sigma for what the fit itself says, which is not the same and\nis the larger of the two whenever the tilt is poorly separated.\n"},"direct_beam_x_pxl":{"type":"number","format":"float","description":"Where the direct beam lands [pixels]. NOT dataset_settings.beam_x_pxl, which is the PONI:\nthe two part company by distance*tan(tilt)/pixel as soon as the detector is tilted.\n"},"direct_beam_y_pxl":{"type":"number","format":"float","description":"Where the direct beam lands, y [pixels]"},"header_distance_mm":{"type":"number","format":"float","description":"The detector distance the input file declared, for comparison [mm]"},"ring_seed_distance_mm":{"type":"number","format":"float","description":"The distance measured from the ring radii before the fit ran [mm]. It is taken from the\nradii, the wavelength and the pixel size alone, so a large gap from header_distance_mm is\nthe answer to the question the calibration was run to ask. Absent when the profile showed\ntoo few rings to fix a scale.\n"},"tilt_refined":{"type":"boolean","description":"Whether the reported rot1/rot2 were measured by this fit. False means they were declined\nand pinned at the input file's values, because the rings could not separate a tilt from a\nshift of the beam centre.\n"},"tilt_significance":{"type":"number","format":"float","description":"How many of its own sigmas the fitted tilt stands from zero. Below about 3 it is not a\nmeasurement of a tilt but of a beam-centre shift, and the tilt is declined. Passing does\nnot certify a tilt: that estimator is limited by systematics rather than by this sigma.\n"},"fit_sigma":{"$ref":"#/components/schemas/powder_calibration_fit_sigma"},"spot_cross_check":{"$ref":"#/components/schemas/powder_calibration_spot_check"}}},"powder_calibration_output":{"type":"object","required":["dataset_settings"],"description":"The result of a powder-ring detector calibration - what rugnux --mode calibration writes as\n<prefix>.json, and what a calibration run over the image buffer would return.\n\ndataset_settings holds the geometry and nothing else, under the property names this API gives\nthem, so it can be POSTed or merged without translating a field. Its beam_x_pxl/beam_y_pxl is\nthe PONI, the foot of the perpendicular from the sample; where the beam actually lands is\ncalibration.direct_beam_x_pxl. The poni_rot*_rad are present whenever any of them is non-zero\nand absent when all are zero, since a body omitting them states a FLAT detector rather than an\nunstated one.\n","properties":{"dataset_settings":{"$ref":"#/components/schemas/dataset_settings"},"calibration":{"$ref":"#/components/schemas/powder_calibration_quality"},"jfjoch_version":{"type":"string","description":"Version of the program that produced this"}}},"calibration_statistics":{"type":"array","items":{"required":["module_number","storage_cell_number","pedestal_g0_mean","pedestal_g1_mean","pedestal_g2_mean","gain_g0_mean","gain_g1_mean","gain_g2_mean","masked_pixels"],"type":"object","properties":{"module_number":{"type":"integer","format":"int64"},"storage_cell_number":{"type":"integer","format":"int64"},"pedestal_g0_mean":{"type":"number","format":"float"},"pedestal_g1_mean":{"type":"number","format":"float"},"pedestal_g2_mean":{"type":"number","format":"float"},"gain_g0_mean":{"type":"number","format":"float"},"gain_g1_mean":{"type":"number","format":"float"},"gain_g2_mean":{"type":"number","format":"float"},"masked_pixels":{"type":"integer","format":"int64"}}}},"jfjoch_statistics":{"type":"object","description":"Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker","properties":{"detector":{"$ref":"#/components/schemas/detector_status"},"detector_list":{"$ref":"#/components/schemas/detector_list"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"image_format_settings":{"$ref":"#/components/schemas/image_format_settings"},"instrument_metadata":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer_settings":{"$ref":"#/components/schemas/file_writer_settings"},"data_processing_settings":{"$ref":"#/components/schemas/spot_finding_settings"},"measurement":{"$ref":"#/components/schemas/measurement_statistics"},"broker":{"$ref":"#/components/schemas/broker_status"},"fpga":{"$ref":"#/components/schemas/fpga_status"},"calibration":{"$ref":"#/components/schemas/calibration_statistics"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"},"pixel_mask":{"$ref":"#/components/schemas/pixel_mask_statistics"},"roi":{"$ref":"#/components/schemas/roi_definitions"},"az_int":{"$ref":"#/components/schemas/azim_int_settings"},"buffer":{"$ref":"#/components/schemas/image_buffer_status"},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"bragg_integration":{"$ref":"#/components/schemas/bragg_integration_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_status"}}},"error_message":{"type":"object","required":["msg","reason"],"properties":{"msg":{"type":"string","description":"Human readable message","example":"Detector in wrong state"},"reason":{"type":"string","description":"Enumerate field for automated analysis","enum":["WrongDAQState","Other"]}}},"roi_azimuthal":{"type":"object","description":"ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector","required":["name","q_min_recipA","q_max_recipA"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"q_min_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Minimum Q-range for the ROI"},"q_max_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Maximum Q-range for the ROI"},"phi_min_deg":{"type":"number","format":"float","description":"Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit both for a full ring. A sector with phi_min_deg > phi_max_deg wraps across 0.\n"},"phi_max_deg":{"type":"number","format":"float","description":"Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.\n"}}},"roi_circle":{"type":"object","description":"Circular ROI","required":["name","center_x_pxl","center_y_pxl","radius_pxl"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"center_x_pxl":{"type":"number","format":"float","description":"X coordinate of center of the circle [pixels]"},"center_y_pxl":{"type":"number","format":"float","description":"Y coordinate of center of the circle [pixels]"},"radius_pxl":{"type":"number","format":"float","minimum":0,"exclusiveMinimum":true,"description":"Radius of the circle [pixels]"}}},"roi_box":{"type":"object","description":"Box ROI","required":["name","min_x_pxl","max_x_pxl","min_y_pxl","max_y_pxl"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"min_x_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in X coordinate for the box","minimum":0},"max_x_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in X coordinate for the box","minimum":0},"min_y_pxl":{"type":"integer","format":"int64","description":"Lower bound (inclusive) in Y coordinate for the box","minimum":0},"max_y_pxl":{"type":"integer","format":"int64","description":"Upper bound (inclusive) in Y coordinate for the box","minimum":0}}},"roi_circle_list":{"type":"object","description":"List of circular ROIs","required":["rois"],"properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_circle"}}}},"roi_box_list":{"type":"object","description":"List of box ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_box"}}}},"roi_azim_list":{"type":"object","description":"List of azimuthal ROIs","properties":{"rois":{"type":"array","maxItems":12,"items":{"$ref":"#/components/schemas/roi_azimuthal"}}}},"roi_definitions":{"type":"object","required":["box","circle","azim"],"description":"ROI defintions","properties":{"box":{"$ref":"#/components/schemas/roi_box_list"},"circle":{"$ref":"#/components/schemas/roi_circle_list"},"azim":{"$ref":"#/components/schemas/roi_azim_list"}}},"dark_mask_settings":{"type":"object","description":"Settings for collection of dark images to be used for mask calculation","required":["detector_threshold_keV","max_allowed_pixel_count","max_frames_with_signal","frame_time_us","number_of_frames"],"properties":{"detector_threshold_keV":{"type":"number","format":"float","description":"Energy threshold for dark image collection","minimum":2.5,"default":3.5,"maximum":100},"frame_time_us":{"type":"integer","format":"int64","description":"Time between frames for dark image collection","minimum":500,"default":10000,"maximum":100000},"number_of_frames":{"type":"integer","format":"int64","description":"Number of frames for dark image collection; 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parameter value affects execution time of FFT"},"fft_high_resolution_A":{"type":"number","format":"float","default":2,"minimum":0.5,"maximum":6,"description":"Sets how finely the FFT samples each search direction: it fixes the extent of the projection\nhistogram, and with it the transform size, so it affects execution time and memory of FFT.\nIt does NOT filter spots - every spot is projected whatever its resolution, so raising it\ndoes not make the transform see a coarser subset of the data.\nThere is also correlation between smallest unit cell and this value, which need to be checked for very small systems.\n"},"fft_num_vectors":{"type":"integer","format":"int64","minimum":128,"default":16384,"description":"Number of search directions for the FFT algorithm; parameter value affects execution time of FFT."},"tolerance":{"type":"number","format":"float","minimum":0,"maximum":0.5,"description":"Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted"},"thread_count":{"type":"integer","format":"int64","minimum":1,"maximum":64,"description":"Thread count for indexing algorithm"},"geom_refinement_algorithm":{"$ref":"#/components/schemas/geom_refinement_algorithm"},"unit_cell_dist_tolerance":{"type":"number","format":"float","minimum":0.0001,"maximum":0.2001,"default":0.05,"description":"Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored"},"viable_cell_min_spots":{"type":"integer","format":"int64","minimum":5,"default":10,"description":"Minimum number of indexed spots required for a cell to be considered viable"},"index_ice_rings":{"type":"boolean","default":false,"description":"Include spots marked as ice rings in the indexing run. \nIf `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.\n"},"rotation_indexing":{"type":"boolean","default":false,"deprecated":true,"description":"Ignored: accepted on input and always returned as false; will be removed in a future release.\nThe Lite and FPGA workflows index each image on its own, rotation or not; rotation indexing is done by rugnux live.\n"},"rotation_indexing_min_angular_range_deg":{"type":"number","format":"float","default":20,"minimum":1,"deprecated":true,"description":"Ignored, as `rotation_indexing`; always returned as 20.0."},"rotation_indexing_angular_stride_deg":{"type":"number","format":"float","default":0.5,"minimum":0,"deprecated":true,"description":"Ignored, as `rotation_indexing`; always returned as 0.5."},"blocking":{"type":"boolean","default":true,"description":"Indexing in Jungfraujoch goes with a dedicated thread pool.\nIf 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.\nIf set to true, the thread pool will block until a thread is available.\n"}}},"instrument_metadata":{"type":"object","description":"Metadata for a measurement instrument","required":["source_name","instrument_name"],"properties":{"source_name":{"type":"string","example":"Swiss Light Source"},"source_type":{"type":"string","description":"Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. \nhttps://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource\nNXsource allows the following:\n\nSpallation Neutron Source\nPulsed Reactor Neutron Source\nReactor Neutron Source\nSynchrotron X-ray Source\nPulsed Muon Source\nRotating Anode X-ray\nFixed Tube X-ray\nUV Laser\nFree-Electron Laser\nOptical Laser\nIon Source\nUV Plasma Source\nMetal Jet X-ray\n","example":"Synchrotron X-ray Source","default":""},"instrument_name":{"type":"string","example":"CristallinaMX"},"pulsed_source":{"type":"boolean","description":"Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)\n","default":false},"electron_source":{"type":"boolean","description":"Settings specific to electron source (e.g., wavelength definition)\n","default":false}}},"detector_module_direction":{"type":"string","enum":["Xp","Xn","Yp","Yn"]},"detector_type":{"type":"string","enum":["EIGER","JUNGFRAU","DECTRIS"]},"image_pusher_type":{"type":"string","default":"None","enum":["ZeroMQ","HDF5","CBOR","TCP","None"]},"standard_detector_geometry":{"type":"object","description":"Regular rectangular geometry, first module is in the bottom left corner of the detector","required":["nmodules"],"properties":{"nmodules":{"type":"integer","minimum":1,"description":"Number of modules in the detector"},"gap_x":{"type":"integer","default":8,"minimum":0,"description":"Gap size in X direction [pixels]"},"gap_y":{"type":"integer","minimum":0,"default":36,"description":"Gap size in Y direction [pixels]"},"modules_in_row":{"type":"integer","minimum":1,"default":1,"description":"Number of modules in one row"}}},"detector_module":{"type":"object","description":"One module of `custom_geometry`: where its readout pixel 0 goes in the assembled image and which way\nits fast and slow readout axes run there.\nFrame: `custom_geometry` is BEFORE `mirror_y` (the image as assembled from the readout); `module_placement`\nis AFTER `mirror_y` (the image as stored, the only one a file reader sees). Same words in both:\n`x0`/`y0` is the image position of the module's readout pixel 0 and `fast_axis`/`slow_axis` say which\nway its fast and slow readout axes run in the image. With `mirror_y` on, a module's entry differs\nbetween the two by the mirror: for an image of height H, y0 (module_placement) = H - 1 - y0\n(custom_geometry), x0 is the same, and Yp and Yn swap in fast_axis/slow_axis. With `mirror_y` off they\nare equal.\n","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number","description":"Image x of the module's readout pixel 0, before mirror_y"},"y0":{"type":"number","description":"Image y of the module's readout pixel 0, before mirror_y"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector_module_placement":{"type":"object","description":"One module of the image and where it lies on the detector plane, as rugnux measures it.\nFrame: `custom_geometry` is BEFORE `mirror_y` (the image as assembled from the readout); `module_placement`\nis AFTER `mirror_y` (the image as stored, the only one a file reader sees). Same words in both:\n`x0`/`y0` is the image position of the module's readout pixel 0 and `fast_axis`/`slow_axis` say which\nway its fast and slow readout axes run in the image. With `mirror_y` on, a module's entry differs\nbetween the two by the mirror: for an image of height H, y0 (module_placement) = H - 1 - y0\n(custom_geometry), x0 is the same, and Yp and Yn swap in fast_axis/slow_axis. With `mirror_y` off they\nare equal.\n`x0`, `y0`, `fast_axis` and `slow_axis` identify the module, whatever the order of the entries, and with\nthe module size they give its box in the image. The plane is in image pixels (a pixel's centre at its\nindex): readout pixel (i, j) - i along the fast axis, j along the slow axis from pixel 0 - lies on it at\n(x0_plane, y0_plane) + i fast_step + j slow_step.\nAs assembled: x0_plane = x0, y0_plane = y0, and each step is the unit vector of its axis\n(Xp = [1, 0], Xn = [-1, 0], Yp = [0, 1], Yn = [0, -1]).\n","required":["x0","y0","fast_axis","slow_axis","x0_plane","y0_plane","fast_step","slow_step"],"properties":{"x0":{"type":"integer","format":"int64","minimum":0,"description":"Image x of the module's readout pixel 0, after mirror_y"},"y0":{"type":"integer","format":"int64","minimum":0,"description":"Image y of the module's readout pixel 0, after mirror_y"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"},"x0_plane":{"type":"number","description":"Plane x of readout pixel 0, in image pixels"},"y0_plane":{"type":"number","description":"Plane y of readout pixel 0, in image pixels"},"fast_step":{"type":"array","items":{"type":"number"},"minItems":2,"maxItems":2,"description":"Plane displacement (x, y) for one pixel along the fast readout axis"},"slow_step":{"type":"array","items":{"type":"number"},"minItems":2,"maxItems":2,"description":"Plane displacement (x, y) for one pixel along the slow readout axis"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER)."},"sensor_thickness_um":{"type":"number","format":"float","minimum":0,"default":320},"readout_time_ns":{"type":"integer","format":"int64","minimum":1,"description":"Minimum difference between frame time and count time in nanoseconds\nDefaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU\n"},"min_count_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum count time available for the detector."},"min_frame_time_ns":{"type":"integer","format":"int64","minimum":0,"description":"Minimum frame time available for the detector."},"calibration_file":{"type":"array","description":"Can be empty for all detectors - default calibration used.\nFor JUNGFRAU: list of gain files, one entry per module.\nFor EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.\n","items":{"type":"string"}},"trim_energies_eV":{"type":"array","description":"List of energies at which trimming calibration is provided.\nOnly needed for PSI EIGER and compulsory in this case\n","items":{"type":"integer","format":"int32","minimum":100}},"hostname":{"type":"array","description":"Hostnames of the detector modules: one entry per module for JUNGFRAU, two per module for EIGER\n(one per half-module). Either empty or the full list.\n","items":{"type":"string"}},"sensor_material":{"type":"string","default":"Si"},"tx_delay":{"type":"array","items":{"type":"integer","format":"int64"}},"base_data_ipv4_address":{"type":"string","example":"10.10.10.50"},"standard_geometry":{"$ref":"#/components/schemas/standard_detector_geometry"},"custom_geometry":{"type":"array","items":{"$ref":"#/components/schemas/detector_module"}},"roi_mode":{"type":"string","default":"","description":"ROI setting for DECTRIS detectors"},"mirror_y":{"type":"boolean","default":true,"description":"Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner"},"temp_thresold_degC":{"type":"integer","format":"int64","description":"Temperature threshold for JUNGFRAU detector modules","minimum":40,"maximum":70,"default":55},"default_settings":{"$ref":"#/components/schemas/detector_settings"}}},"zeromq_settings":{"type":"object","description":"ZeroMQ configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"send_watermark":{"type":"integer","format":"int64","minimum":2,"maximum":16384,"default":100,"description":"Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)"},"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for ZeroMQ socket"},"image_socket":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets.  \nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"},"writer_notification_socket":{"type":"string","example":"tcp://1.3.4.6:7000","description":"PULL ZeroMQ socket for notifications from writer that it finished operation. \nThis allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous.\nUsing * (star) instead of port number is allowed and it means a random free port number.\n"}}},"tcp_settings":{"type":"object","description":"TCP image stream configuration for Jungfraujoch software.\nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","required":["image_socket"],"properties":{"send_buffer_size":{"type":"integer","format":"int64","description":"Send buffer size for TCP/IP socket"},"image_socket":{"type":"string","example":"tcp://1.2.3.4:5000","description":"tcp://<IP address>:<port>\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces\n"},"nwriters":{"type":"integer","format":"int64","minimum":1,"maximum":100,"default":32,"description":"Number of TCP/IP writers to be used for streaming images"},"peer_liveness_timeout_ms":{"type":"integer","format":"int64","description":"Max time (in milliseconds) a send may block with no sign of life from the\nwriter (no BUSY heartbeat or ACK) before the connection is declared dead.\nOptional; the built-in default is used when unset.\n"},"max_backpressure_timeout_ms":{"type":"integer","format":"int64","description":"Hard upper bound (in milliseconds) on backpressure: if no bytes can be sent to\nthe writer for this long the connection is declared dead even while the writer\nkeeps heartbeating, so a wedged writer cannot block the run or its\nfinalization. Optional; the built-in default is used when unset.\n"}}},"pcie_devices":{"type":"array","minItems":1,"items":{"type":"object","required":["blk"],"properties":{"blk":{"type":"string","example":"/dev/jfjoch0","description":"Block device name"},"ipv4":{"type":"string","example":"10.1.1.7","description":"IPv4 address of the block device"}}}},"bragg_integration_settings":{"type":"object","description":"Settings for Bragg spot integration, used by rugnux live (the Lite and FPGA workflows do not integrate)","required":["integration_model"],"properties":{"integration_model":{"$ref":"#/components/schemas/integration_model"},"max_hkl":{"type":"integer","minimum":1,"maximum":511,"default":100,"description":"How far the Bragg predictor walks the lattice: reflections with |h|,|k|,|l| above this are\nnever predicted. An axis is truncated once a/d_min exceeds it, so a long axis - or a short\none taken to high resolution - loses its outermost reflections. The cost grows as the cube\n(2n+1)^3 of candidates per image, which is why online keeps a fixed, predictable value\ninstead of taking it from whichever crystal is mounted.\n\nOmitting the field selects the default above; it is never interpreted as \"choose per\ncrystal\". The offline tools (rugnux, viewer) do derive it from the refined cell when it is\nleft unset there, but that is their own default and is not reachable through this API.\n"}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minItems":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"bragg_integration":{"$ref":"#/components/schemas/bragg_integration_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"},"rugnux":{"$ref":"#/components/schemas/rugnux_settings"}}},"rugnux_settings":{"type":"object","description":"Rugnux live mode: rotation collections from a DECTRIS detector are processed by rugnux\ninside the broker while they arrive, and the merged result is sent to the writer. Serial\ncollections, from a DECTRIS detector or converted by the FPGA (JUNGFRAU), are analysed on the GPU\nafter a pre-pass on their first images that decides the beam centre, distance and mask (`stills` in\n`/rugnux/status`), and merged as they go.\n","properties":{"enable":{"type":"boolean","default":false,"description":"Process DECTRIS rotation collections with rugnux live, and serial collections on the GPU after a pre-pass"},"reserved_cpus":{"type":"integer","format":"int64","minimum":0,"default":4,"description":"CPU threads left to the receiver and the image pusher while rugnux runs"},"deadline_s":{"type":"number","format":"double","minimum":0,"default":60,"description":"Fixed cutoff: this long after the last image the analysis is cut, and the collection ends\nwith what it has established (as `POST /cancel` after the last image does). 0 means no cutoff.\n"}}},"rugnux_status":{"type":"object","required":["enable","reserved_cpus","model_loaded"],"properties":{"enable":{"type":"boolean","description":"Rugnux live mode is enabled"},"reserved_cpus":{"type":"integer","format":"int64","description":"CPU threads left to the receiver and the image pusher while rugnux runs"},"deadline_s":{"type":"number","format":"double","description":"Seconds after the last image at which the analysis is cut; 0 means no cutoff"},"model_loaded":{"type":"boolean","description":"A model was uploaded with `PUT /config/rugnux/model`"},"model_size_bytes":{"type":"integer","format":"int64","description":"Size of the uploaded model file"}}},"rugnux_live_step":{"type":"object","required":["title","started_s","notes"],"properties":{"title":{"type":"string"},"started_s":{"type":"number","format":"double","description":"Start of the step, since the first image (negative if before it)"},"duration_s":{"type":"number","format":"double","description":"Set once the next step starts or the run ends"},"notes":{"type":"array","description":"What the step found (e.g. lattice, space group)","items":{"type":"string"}}}},"rugnux_summary_row":{"type":"object","required":["label","value"],"properties":{"label":{"type":"string"},"value":{"type":"string"}}},"rugnux_triage_item":{"type":"object","description":"A line of the pathology checklist of `_report.txt` (its SUMMARY), in the report's words.\n`ok`: looked for and not found; `attention`: its warning fired (its codes are in the report's\nPATHOLOGY_FLAGS); `serious`: a pathology that leaves no result to use - no lattice, or a merge without\nsignal (the report's verdict FAILED or UNUSABLE); `not_measured`: it could not be looked for on this run.\n","required":["label","codes","severity","text"],"properties":{"label":{"type":"string","description":"Name of the condition, e.g. \"Twinning\" - the summary row's label"},"codes":{"type":"array","description":"The PATHOLOGY_FLAGS codes the line stands for, e.g. TWINNING","items":{"type":"string"}},"severity":{"type":"string","enum":["ok","attention","serious","not_measured"]},"text":{"type":"string","description":"The summary row's own words; empty where it has none"},"detail":{"type":"string","description":"The report's warnings that fired for it, one per line; absent where none fired"}}},"rugnux_live_model":{"type":"object","description":"What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The\nR-factors here are those of the placed model with its own coordinates and B factors; what refinement made\nof it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by\nmolecular replacement.\n","required":["placement","model_name","predicted","reason","mr_decision","mr_space_group","anomalous_site"],"properties":{"placement":{"type":"string","description":"RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED"},"model_name":{"type":"string"},"predicted":{"type":"boolean","description":"Searched for as a predicted model"},"reason":{"type":"string","description":"Why the model could not be searched for or validated; empty otherwise"},"r_work":{"type":"number","format":"double"},"r_free":{"type":"number","format":"double"},"cc_model":{"type":"number","format":"double","description":"Correlation of the merged intensities with the placed model's, over all reflections"},"fit_sigma":{"type":"number","format":"double","description":"How far R-work stands below that of the same model in random orientations, in standard deviations"},"map_atom_sigma":{"type":"number","format":"double","description":"Mean 2mFo-DFc value at the atom centres, in map sigma"},"rigid_body_angle_deg":{"type":"number","format":"double"},"rigid_body_shift_A":{"type":"number","format":"double"},"mr_decision":{"type":"string","description":"Molecular replacement's decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run"},"mr_space_group":{"type":"string","description":"The group molecular replacement placed the model in; empty where it placed none"},"copies":{"type":"integer","format":"int64","description":"Copies placed by molecular replacement"},"tf_z":{"type":"number","format":"double","description":"Translation-function Z-score, the highest of the copies'"},"rf_z":{"type":"number","format":"double","description":"Rotation-function Z-score of the first copy's orientation"},"llg_z":{"type":"number","format":"double","description":"Likelihood Z-score after the rigid body, where a copy's translation function did not stand out"},"mr_d_min":{"type":"number","format":"double","description":"High-resolution limit of the molecular-replacement search, in Angstrom"},"anomalous_site":{"type":"string","description":"Atom with the strongest anomalous difference density, e.g. \"SG CYS A7\"; empty where there is no anomalous map"},"anomalous_site_sigma":{"type":"number","format":"double","description":"Anomalous difference density at that atom, in map sigma"},"refinement":{"$ref":"#/components/schemas/rugnux_live_refinement"}}},"rugnux_live_refinement":{"type":"object","description":"The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set\nwhere a placed model was refined or its refinement failed; absent where the model was not placed or\nrefinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline\nor cancel can cut it.\n","required":["performed","cancelled","reason","on_gpu","seconds","blob_count","blobs"],"properties":{"performed":{"type":"boolean","description":"Refinement ran; false with `reason` where it failed"},"cancelled":{"type":"boolean","description":"The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the\nrest left out (cut before the first, the model is the placement's)\n"},"reason":{"type":"string","description":"Why refinement did not run to the end; empty otherwise"},"on_gpu":{"type":"boolean"},"seconds":{"type":"number","format":"double","description":"Wall time of the refinement"},"r_work":{"type":"number","format":"double","description":"R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)"},"r_free":{"type":"number","format":"double","description":"R-free of the refined model, on the same reflections as `r_work`"},"rmsd_bonds_A":{"type":"number","format":"double","description":"RMS deviation of the bond lengths from the dictionary, where the restrained stage ran"},"rmsd_angles_deg":{"type":"number","format":"double","description":"RMS deviation of the bond angles from the dictionary, where the restrained stage ran"},"blob_count":{"type":"integer","format":"int64","description":"Unexplained blobs of the refined model's mFo-DFc map (above 3 sigma, peaking above 4)"},"blobs":{"type":"array","description":"The strongest blobs, at most 50, strongest first","items":{"$ref":"#/components/schemas/rugnux_live_blob"}}}},"rugnux_live_blob":{"type":"object","description":"A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on\nwhat is measured, to point a person at the density - not an identification.\n","required":["kind","x","y","z","peak_sigma","volume_A3","nearest_atom"],"properties":{"kind":{"type":"string","enum":["WATER","ION","LIGAND","MODEL_ERROR","UNASSIGNED"]},"x":{"type":"number","format":"double","description":"Centroid, Cartesian Angstrom, in the frame of the refined model (`/rugnux/model.cif`)"},"y":{"type":"number","format":"double"},"z":{"type":"number","format":"double"},"peak_sigma":{"type":"number","format":"double","description":"The highest point, in map sigma"},"volume_A3":{"type":"number","format":"double","description":"Volume above 3 sigma, in cubic Angstrom"},"nearest_atom":{"type":"string","description":"e.g. \"OG1 THR A42\""},"nearest_atom_distance_A":{"type":"number","format":"double","description":"Absent where no atom is within 12 Angstrom"}}},"rugnux_live_stills":{"type":"object","description":"Serial frames analysed on the GPU: the pre-pass on the first images (the beam\ncentre, distance and mask the whole collection is analysed with), and the analysis since.\n","required":["prepass","images_held","images_needed","file_beam_x_pxl","file_beam_y_pxl","file_distance_mm","images_analysed","images_indexed"],"properties":{"prepass":{"type":"string","enum":["Holding","Running","Done","Failed"],"description":"Holding the first images, running on them, or done (Failed - the stated geometry and mask are used)"},"images_held":{"type":"integer","format":"int64","description":"Images held for the pre-pass"},"images_needed":{"type":"integer","format":"int64","description":"Images the pre-pass runs on"},"prepass_s":{"type":"number","format":"double","description":"How long the pre-pass took"},"file_beam_x_pxl":{"type":"number","format":"double"},"file_beam_y_pxl":{"type":"number","format":"double"},"file_distance_mm":{"type":"number","format":"double"},"beam_x_pxl":{"type":"number","format":"double","description":"Beam centre the pre-pass decided (where the beam lands)"},"beam_y_pxl":{"type":"number","format":"double"},"distance_mm":{"type":"number","format":"double","description":"Detector distance the pre-pass decided"},"shadow_pixels":{"type":"integer","format":"int64","description":"Pixels masked as the beam-stop shadow"},"bad_pixels":{"type":"integer","format":"int64","description":"Pixels masked as defective (hot, dead, error value)"},"images_analysed":{"type":"integer","format":"int64"},"images_indexed":{"type":"integer","format":"int64"},"analysis_rate_hz":{"type":"number","format":"double","description":"Images analysed per second since the pre-pass"}}},"rugnux_live_shell":{"type":"object","description":"A resolution shell of the merge: a row of the shell table of `_report.txt`, with R_split from its serial\nstatistics and R-free from its MODEL VALIDATION, on the same shells. Fractions, not percent. A quantity\nnot measured for this shell or this run is absent.\n","required":["d_min","d_max","n_obs","n_unique"],"properties":{"d_min":{"type":"number","format":"double","description":"High-resolution limit of the shell, in Angstrom (the row label of the report's table)"},"d_max":{"type":"number","format":"double","description":"Low-resolution limit of the shell, in Angstrom"},"n_obs":{"type":"integer","format":"int64","description":"Observations merged"},"n_unique":{"type":"integer","format":"int64","description":"Unique reflections"},"completeness":{"type":"number","format":"double"},"multiplicity":{"type":"number","format":"double"},"i_over_sigma":{"type":"number","format":"double","description":"Mean I/sigma(I) of the merged reflections"},"r_meas":{"type":"number","format":"double","description":"Rotation only, as in the report"},"cc_half":{"type":"number","format":"double","description":"CC1/2 of the shell table"},"cc_ref":{"type":"number","format":"double","description":"CC against the reference data, where reference data were given"},"r_split":{"type":"number","format":"double","description":"Serial data only, with every frame whole in one half-set"},"r_free":{"type":"number","format":"double","description":"R-free of the placed model (as given, not refined) over the shell's free reflections"}}},"rugnux_live_frame_range":{"type":"object","description":"A stretch of a rotation sweep the merge did not take at face value: downgraded (merged at the reduced\nweight its own scale and sigmas give it) or rejected (nothing of it reached the merge), with the\nreason the sweep-quality diagnostic saw - the lines of the report's SWEEP section.\n","required":["first_image","last_image","disposition","reason"],"properties":{"first_image":{"type":"integer","format":"int64","description":"First image of the stretch, inclusive, numbered as the collection's images"},"last_image":{"type":"integer","format":"int64","description":"Last image of the stretch, inclusive"},"disposition":{"type":"string","enum":["downgraded","rejected"]},"reason":{"type":"string","description":"What was seen over the stretch, e.g. \"out of beam\", \"no diffraction\", \"radiation damage\""}}},"rugnux_live_status":{"type":"object","description":"Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`.\nTimes are taken when the image puller received a message, and are in seconds since the first image\n(before it arrives, since now). The frame rate is `(images_received - 1) / last_image_s`.\n","required":["state","message","images_expected","images_received","elapsed_s","steps","verdict","verdict_text","summary","warnings","probe","placed_model","refined_model","anomalous_map","anomalous_signal"],"properties":{"state":{"type":"string","enum":["Idle","Running","Done","Failed","Cancelled","Skipped"]},"placed_model":{"type":"boolean","description":"The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from\n`/rugnux/map.ccp4`.\n"},"refined_model":{"type":"boolean","description":"The run refined the placed model: `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and\nits maps unless asked for `stage=placed`.\n"},"anomalous_map":{"type":"boolean","description":"The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map\n(`/rugnux/map.ccp4?type=anom`).\n"},"anomalous_signal":{"type":"boolean","description":"The merged data carry usable anomalous signal (the summary's \"Anomalous\" row says so)"},"model":{"$ref":"#/components/schemas/rugnux_live_model"},"stills":{"$ref":"#/components/schemas/rugnux_live_stills"},"shells_merge":{"type":"string","description":"Which merge `shells` are of - \"the collection\", or on serial data a provisional merge such as\n\"50% of the images (provisional)\"; absent until there is a merge\n"},"shells":{"type":"array","description":"Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of\n`_report.txt`. Rotation: once the run is over; serial: at each provisional merge and at the end.\n`overall` is the same table's \"Overall\" row (whole-merge completeness, multiplicity, I/sigma, CC1/2,\nR_meas or R_split, CCref, and the overall R-free of the model validated on it), present with `shells`.\n","items":{"$ref":"#/components/schemas/rugnux_live_shell"}},"overall":{"$ref":"#/components/schemas/rugnux_live_shell"},"frame_scales":{"type":"array","description":"Rotation, once the run is over: the per-image scale factor of the merge, one entry per image of the\ncollection in its order, 0 where the image got none (not indexed, or rejected). Absent on serial\ndata and until there is a merge.\n","items":{"type":"number","format":"float"}},"frame_ranges":{"type":"array","description":"Rotation, once the run is over: the stretches of the sweep the merge downgraded or rejected, in\norder; every image outside them is merged at its own weight. Absent on serial data and until there\nis a merge; empty where the whole sweep was merged.\n","items":{"$ref":"#/components/schemas/rugnux_live_frame_range"}},"space_group":{"type":"string","description":"Space group of the result (the summary's \"Space group\" row); absent until the run is over"},"d_min":{"type":"number","format":"double","description":"High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge"},"isa":{"type":"number","format":"double","description":"ISa of the error model; absent until the run is over, or where it was not determined"},"probe":{"type":"string","description":"Answer of the early lattice probe on the first 60 degrees; empty until it answers"},"probe_s":{"type":"number","format":"double","description":"When the probe answered, since the first image"},"start_to_first_image_s":{"type":"number","format":"double","description":"From the START message to the first image; set once the first image arrives"},"message":{"type":"string","description":"Why the run failed or was skipped"},"images_expected":{"type":"integer","format":"int64"},"expected_collection_s":{"type":"number","format":"double","description":"How long the collection is set up to take - images_expected times the image time; absent if not known"},"images_received":{"type":"integer","format":"int64"},"elapsed_s":{"type":"number","format":"double"},"step_progress":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"Fraction of the current pass's images"},"steps":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_live_step"}},"last_image_s":{"type":"number","format":"double","description":"When the last image arrived, since the first image; set once the collection is over"},"cut":{"type":"string","description":"Empty, or why the analysis was cut: `deadline` (`deadline_s` after the last image) or `cancel`\n(`POST /cancel`). The end message then carried what was established at the cut.\n"},"cut_s":{"type":"number","format":"double","description":"When the analysis was cut, since the first image"},"last_image_to_written_s":{"type":"number","format":"double","description":"From the last image received to all results written"},"verdict":{"type":"string","description":"OK, WARNINGS, UNUSABLE, FAILED or CANCELLED; empty until the run is over"},"verdict_text":{"type":"string"},"summary":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_summary_row"}},"warnings":{"type":"array","items":{"type":"string"}},"triage":{"type":"array","description":"The pathology checklist of the report, in its order. Rotation: once the run is over; serial: at each\nprovisional merge and at the end. Absent until there is one.\n","items":{"$ref":"#/components/schemas/rugnux_triage_item"}}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\nIt also clears the image buffer, the previous collection's plots and live rugnux status, disables live rugnux analysis and removes the rugnux model.\nIt drops the previous dataset's bearer tokens and resets its settings, so nothing of that dataset stays readable.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\nOptional `tokens` protect the dataset: while set, its statistics, buffered images and plots\nrequire `Authorization: Bearer <token>`.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately.\nThe operation that finished either succeeded, was cancelled, or ended with a warning.\n"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code, or the operation that finished ended in an error -\nmissing packets, or a writer that could not write - see output message.\nA cancelled data collection is not an error.\n","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nWith rugnux live mode (`/config/rugnux`) the command also cuts the rugnux analysis, during the collection\nor after its last image alike: the collection ends with what the analysis has established\n(see `cut` in `/rugnux/status`). After the last image the collection itself is complete and is not\nmarked as cancelled.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/bragg_integration":{"put":{"summary":"Change Bragg integration settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get Bragg integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/rugnux":{"put":{"summary":"Change rugnux live mode settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get rugnux live mode settings and model status","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_status"}}}}}}},"/config/rugnux/model":{"put":{"summary":"Upload the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\nThe model (PDB or mmCIF, optionally gzipped; at most 64 MiB) is used for molecular replacement\nand validation of every following rugnux live collection, until it is removed with\n`DELETE /config/rugnux/model` or replaced by another upload.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Empty body, or not a model that can be read (PDB or mmCIF, optionally gzipped)"},"413":{"description":"Model larger than 64 MiB"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"delete":{"summary":"Remove the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/rugnux/status":{"get":{"summary":"Get live rugnux processing status of the last collection","description":"Can be done anytime","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_live_status"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/rugnux/model.cif":{"get":{"summary":"Get the model as placed by the last rugnux live run","description":"The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the\n`_model.cif` file written beside the data: the data's cell and space group, with the input model's own\nmetadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.\nWhere the run refined the model, the refined model unless asked for `stage=placed`.\n","parameters":[{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model, or (`stage=refined`) refined none"}}}},"/rugnux/map.ccp4":{"get":{"summary":"Get an electron-density map of the last rugnux live run","description":"The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map\ncoefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where\nthe model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and\nRMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run\nrefined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;\nthe anomalous map stays on the placed model's phases.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc","anom"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map,\n(F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map`\nin `/rugnux/status`)\n"},{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type or stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs, or (`stage=refined`) refined none"}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - 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no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","description":"`measurement` is omitted unless the request carries a valid bearer token for a protected\ndataset (see `tokens` in `/start`).\n","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection (dataset name, unit cell, ...)","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - 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see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask.tiff":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (TIFF)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\nUser mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.\n","requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Not a valid single-channel TIFF or size doesn't match the detector"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/preview/pedestal.tiff":{"get":{"parameters":[{"in":"query","name":"gain_level","required":true,"schema":{"type":"integer"},"description":"Gain level (0, 1, 2)"},{"in":"query","name":"sc","schema":{"type":"integer"},"description":"Storage cell number"}],"summary":"Get pedestal in TIFF format","responses":{"200":{"description":"Calibration image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Invalid gain level or storage cell number"},"404":{"description":"No calibration recorded so far"}}}},"/preview/plot":{"get":{"summary":"Generate 1D plot from Jungfraujoch","parameters":[{"$ref":"#/components/parameters/binning"},{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/fill_value"},{"$ref":"#/components/parameters/experimental_coord"},{"$ref":"#/components/parameters/azint_unit"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/plots"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/preview/plot.bin":{"get":{"summary":"Generate 1D plot from Jungfraujoch and send in raw binary format.\nData are provided as (32-bit) float binary array.\nThis format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.\n","parameters":[{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/roi"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/result/scan":{"get":{"summary":"Get full scan result","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/scan_result"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No grid scan recorded"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/start.cbor":{"get":{"summary":"Get Start message in CBOR format","description":"Contains metadata for a dataset (e.g., experimental geometry)","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Return start message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No measurement so far"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/live/events":{"get":{"summary":"Event stream of the collection, for a reader following it","description":"Server-sent events (text/event-stream) for the current collection, from the moment /start has\naccepted it: first its whole history, then every change, until it ends or a new collection\nbegins. Only one reader at a time. Events, each with a JSON `data` line:\n- `start` {run_number, run_name, file_prefix, number_of_images, images_per_file, cbor} - first,\n  once the start message is known: at once for a JUNGFRAU, when the detector sends its own for\n  a DECTRIS. `cbor` is the start message the writer of the master file received, CBOR in base64;\n  a reader builds the dataset from it;\n- `file` {file_number, file, first_image, image_count} - a data file closed and renamed into\n  place; `file` is relative to the collection's root, as the writer named it;\n- `end` {images, error?} - every writer acknowledged the end: the data files and the master\n  file are in place; `images` is the number of images collected. Also sent, with `error`, when\n  the measurement ends any other way - before the start message, for one. The stream then closes;\n- `superseded` {run_number} - a new collection began. The stream then closes.\nA comment line (`: keepalive`) every 10 s when nothing happens.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Event stream","content":{"text/event-stream":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No collection has started"},"409":{"description":"Another reader is following the collection, or the image pusher does not report closed data files"}}}},"/image_buffer/image.cbor":{"get":{"summary":"Get image message in CBOR format","description":"Contains full image data and metadata. The image must come from the latest data collection.","parameters":[{"$ref":"#/components/parameters/image_id"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Return image message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.jpeg":{"get":{"summary":"Get preview image in JPEG format using custom settings","parameters":[{"$ref":"#/components/parameters/image_id"},{"$ref":"#/components/parameters/show_user_mask"},{"$ref":"#/components/parameters/show_roi"},{"$ref":"#/components/parameters/show_spots"},{"$ref":"#/components/parameters/show_predictions"},{"$ref":"#/components/parameters/show_beam_center"},{"$ref":"#/components/parameters/saturation"},{"$ref":"#/components/parameters/jpeg_quality"},{"$ref":"#/components/parameters/resolution_ring"},{"$ref":"#/components/parameters/color_scale"},{"$ref":"#/components/parameters/resolution_estimate"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Preview image","content":{"image/jpeg":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"Image not present in the buffer - either not yet measured or already replaced by a next image."},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/image.tiff":{"get":{"summary":"Get preview image in TIFF format","parameters":[{"$ref":"#/components/parameters/image_id"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Preview image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No preview image recorded so far"}}}},"/image_buffer/clear":{"post":{"summary":"Clear image buffer","description":"Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.","responses":{"200":{"description":"Done"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/status":{"get":{"summary":"Get status of the image buffers","description":"Can be run at any stage of Jungfraujoch operation, including during data collection.\nThe status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,\nthen image might be replaced in the buffer between calling /images and /image.cbor.\n","responses":{"200":{"description":"Done","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_buffer_status"}}}},"500":{"description":"Error within Jungfraujoch code - see output 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A dataset started without `tokens` is not protected and the header is ignored.\n"}},"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","spindle_blind_fraction","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","compression_ratio","ice_ring_score"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. 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Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees. 0 for an axis that does not turn: the axis then\nrecords the angle the spindle stood at, which is how a grid scan or a set of stills\nstates its head position.\n"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\nFlex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).\n","enum":["BeamCenter","OrientationOnly","Flex","None"]},"integration_model":{"type":"string","description":"Bragg spot integration model.\nProfileGaussian - profile fit with a measured-width Gaussian (Kabsch-style), the default; more\n  accurate intensities than box summation.\nProfileEmpirical - profile fit with a per-resolution-shell empirical profile learned from strong spots.\nBoxSum - classical uniform box summation minus a ring-mean background; the simpler, faster fallback.\n","enum":["ProfileGaussian","ProfileEmpirical","BoxSum"],"default":"ProfileGaussian"},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. 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Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","bszstd_rlehuf","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","minimum":0,"description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"beam_size_x_um":{"type":"number","format":"float","minimum":0,"description":"First element of /entry/instrument/beam/incident_beam_size in NXmx\nHorizontal size of the X-ray beam where it meets the sample - the FWHM of a focused beam,\nthe full width of a slit-defined one. [um]\n"},"beam_size_y_um":{"type":"number","format":"float","minimum":0,"description":"Second element of /entry/instrument/beam/incident_beam_size in NXmx\nVertical size of the X-ray beam where it meets the sample. [um]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments\nand to turn off for other experiments.\n"},"save_calibration":{"type":"boolean","description":"Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.\nIf parameter is not provided calibration will be saved only if more than 4 images are recorded.\n"},"polarization_factor":{"type":"number","description":"Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization","format":"float","minimum":-1,"maximum":1},"ring_current_mA":{"type":"number","format":"float","description":"Ring current at the beginning of the data collection","minimum":0},"sample_temperature_K":{"type":"number","format":"float","description":"Sample temperature in Kelvin","minimum":0},"poni_rot1_rad":{"type":"number","description":"PONI angle rot1 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot2_rad":{"type":"number","description":"PONI angle rot2 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot3_rad":{"type":"number","description":"PONI angle rot3 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"unit_cell":{"$ref":"#/components/schemas/unit_cell"},"spot_finding":{"type":"boolean","description":"Enable spot finding and save spots","default":true},"smargon":{"type":"object","description":"Geometry of Smargon goniometer at SLS 2.0 / MX beamlines. \nAssuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.\n","required":["phi_deg","chi_deg"],"properties":{"phi_deg":{"type":"number","format":"float","description":"Phi angle in degrees"},"chi_deg":{"type":"number","format":"float","description":"Chi angle in degrees"},"phi_axis":{"type":"array","description":"Phi rotation axis","default":[1,0,0],"example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"chi_axis":{"type":"array","description":"Chi rotation axis","default":[0,0,1],"example":[0,0,1],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3}}},"max_spot_count":{"type":"integer","minimum":10,"maximum":2000,"default":250,"description":"Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected"},"detect_ice_rings":{"type":"boolean","description":"Flag spots as ice rings and reduce their effect on indexing. Left out, the broker's own\nspot finding treats no spot as an ice ring, rugnux live decides as a bare `rugnux` would (on\nfor a rotation sweep, off for stills), and the master file carries no `detect_ice_rings`.\n"},"async_start":{"type":"boolean","default":false,"description":"When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement."},"module_placement":{"type":"array","items":{"$ref":"#/components/schemas/detector_module_placement"},"description":"Where the detector's modules lie for this dataset, as rugnux measures them: rugnux writes\n`<prefix>_module_placement.json`, which holds exactly this field, to be merged into the dataset settings.\nEach entry names its module by its readout pixel 0 and readout axes in the stored image (`x0`, `y0`,\n`fast_axis`, `slow_axis`, after `mirror_y`; see `detector_module_placement`), in any order; every\nmodule must be named once, and only modules of the detector, else `/start` fails with 400. The image\nis assembled as configured (`custom_geometry`); the placement goes into the start message and the\nNXmx `module_NN` groups, and the analysis takes it. Omitted or empty:\nmodules as assembled.\n"},"tokens":{"type":"array","items":{"type":"string","minLength":1},"writeOnly":true,"description":"Bearer tokens that protect this dataset: any number, all equivalent (e.g. a beamline\nsecret and a dataset-specific user secret). While set, the endpoints marked with the\n`bearerAuth` security scheme require `Authorization: Bearer <token>` and answer 401 otherwise.\nEvery accepted `/start` replaces the previous dataset's tokens; omitted or empty means no\nprotection. Never returned by any endpoint.\n"},"xray_fluorescence_spectrum":{"type":"object","required":["energy_eV","data"],"properties":{"energy_eV":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan energy for each measurement point"},"data":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV"}}}}},"crystal_lattice":{"type":"array","items":{"type":"number","format":"float"},"minItems":9,"maxItems":9,"description":"Real-space crystal lattice 3D vectors in Angstrom.\nOrder is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)\n"},"unit_cell":{"type":"object","description":"Unit cell parameters. Necessary to run indexing. Units of angstrom and degree","required":["a","b","c","alpha","beta","gamma"],"properties":{"a":{"type":"number","format":"float","example":37,"minimum":0},"b":{"type":"number","format":"float","example":37,"minimum":0},"c":{"type":"number","format":"float","example":78,"minimum":0},"alpha":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"beta":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"gamma":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360}}},"file_writer_format":{"type":"string","enum":["NXmxOnlyData","NXmxLegacy","NXmxVDS","NXmxIntegrated","CBF","TIFF","NoFileWritten"],"default":"NXmxVDS","description":"NoFileWritten - no files are written at all\nNXmxOnlyData - only data files are written, no master file\nNXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia\nNXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling\nNXmxIntegrated - single HDF5 per dataset\nCBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\nTIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\n"},"file_writer_settings":{"type":"object","properties":{"overwrite":{"type":"boolean","default":false,"description":"Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.\n"},"format":{"$ref":"#/components/schemas/file_writer_format"}}},"pixel_mask_statistics":{"type":"object","properties":{"user_mask":{"description":"Number of pixels masked using the user mask","type":"integer","format":"int64","minimum":0},"too_high_pedestal_rms":{"description":"Number of pixels with G0 pedestal RMS higher than provided threshold","type":"integer","format":"int64","minimum":0},"wrong_gain":{"description":"Number of pixels that show wrong gain level during the pedestal procedure","type":"integer","format":"int64","minimum":0}}},"image_buffer_status":{"type":"object","required":["image_numbers","total_slots","in_preparation_slots","in_sending_slots","available_slots","max_image_number","min_image_number"],"properties":{"min_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Smallest image number available in the buffer"},"max_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Largest image number available in the buffer"},"image_numbers":{"type":"array","description":"Image numbers currently present in the buffer.","items":{"type":"integer","format":"int64"}},"total_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer. This number, compared to number of images in data collection and\nframe rate will determine \"retention\" rate of the image buffer.\n"},"available_slots":{"type":"integer","format":"int64","description":"Slots available for the data collection"},"in_preparation_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently in preparation for sending.\n"},"in_sending_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently sending/writing data.\n"},"current_counter":{"type":"integer","format":"int64","description":"Counter of changes in the image buffer - either new start message or new image added.\nFor optimization one can only load new images/datasets from the HTTP if this value changes.\nCounter is optional as it was not implemented in older versions to avoid breaking change\n"}}},"image_format_settings":{"type":"object","required":["summation","jungfrau_conversion","geometry_transform","mask_chip_edges","mask_module_edges","apply_mask"],"properties":{"summation":{"type":"boolean","description":"Enable summation of images to a given image_time\nIf disabled images are saved according to original detector speed, but image count is adjusted\n"},"geometry_transform":{"type":"boolean","description":"Place module read-out into their location on composed detector and extend multipixels\n"},"jungfrau_conversion":{"type":"boolean","description":"Convert pixel value in ADU to photon counts/energy\nOnly affects JUNGFRAU detector\n"},"jungfrau_conversion_factor_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to convert energy deposited into pixel to counts\nIf not provided incident_energy_keV is used\n"},"bit_depth_image":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of resulting image (it doesn't affect the detector read-out value)\nIf not provided value is adjusted automatically\n"},"signed_output":{"type":"boolean","description":"Controls if pixels have signed output\nIf not provided value is adjusted automatically\n"},"mask_module_edges":{"type":"boolean","default":true,"description":"Mask 1 pixel on the module boundary\n"},"mask_chip_edges":{"type":"boolean","default":true,"description":"Mask multipixels on chip boundary\n"},"jungfrau_mask_pixels_without_g0":{"type":"boolean","default":true,"description":"JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.\nThis should be turned off for cases, where detector is operated at room temperature with long exposure time.\n"},"apply_mask":{"type":"boolean","default":false,"description":"Masked pixels are set to special value in the images produced by Jungfraujoch\n"},"jungfrau_pedestal_g0_rms_limit":{"type":"integer","format":"int64","default":100,"minimum":0,"description":"Pixels with pedestal G0 RMS above the threshold are marked as masked pixels"}}},"detector_power_state":{"type":"string","description":"Power on of ASICs","enum":["PowerOn","PowerOff","Partial"]},"detector_state":{"type":"string","description":"Current state of the detector","enum":["Idle","Waiting","Busy","Error","Not connected"]},"detector_status":{"type":"object","required":["state","powerchip","server_version","number_of_triggers_left","fpga_temp_degC","high_voltage_V"],"properties":{"state":{"$ref":"#/components/schemas/detector_state"},"powerchip":{"$ref":"#/components/schemas/detector_power_state"},"server_version":{"type":"string","description":"Detector server (on read-out boards) version"},"number_of_triggers_left":{"type":"integer","format":"int64","description":"Remaining triggers to the detector (max of all modules)"},"fpga_temp_degC":{"type":"array","description":"Temperature of detector FPGAs","items":{"type":"integer","format":"int64"}},"high_voltage_V":{"type":"array","description":"High voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real detector"},"internal_frame_generator_images":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":64,"description":"Number of images stored in the internal frame generator."},"detector_trigger_delay_ns":{"type":"integer","format":"int64","minimum":0,"default":0,"description":"Delay between TTL trigger and acquisition start [ns]"},"timing":{"$ref":"#/components/schemas/detector_timing"},"eiger_threshold_keV":{"type":"number","format":"float","minimum":1,"maximum":100,"description":"Threshold for the PSI EIGER detector and all DECTRIS detectors.\nIf value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.\nIf value is not provided, threshold will be determined on start of acquisition as half of incident energy. \nThis might lead to increased start time.\n"},"eiger_bit_depth":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of PSI EIGER read-out. This is  \nIf value is not provided, depth will be determined based on the image time:\n* Exposure time < 500 microseconds depth of 8 bit will be used,\n* 500 <= exposure time < 2622 microseconds depth of 16 bit will be used\n* Exposure time >= 2622 microseconds depth of 32 bit will be used.\n"},"jungfrau_pedestal_g0_frames":{"type":"integer","format":"int64","default":2000,"minimum":0},"jungfrau_pedestal_g1_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_g2_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_min_image_count":{"type":"integer","format":"int64","default":128,"minimum":32,"description":"Minimum number of collected images for pedestal to consider it viable"},"jungfrau_storage_cell_count":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":16},"jungfrau_storage_cell_delay_ns":{"type":"integer","format":"int64","minimum":2100,"default":5000,"description":"Delay between two storage cells [ns]"},"jungfrau_fixed_gain_g1":{"type":"boolean","default":false,"description":"Fix gain to G1 (can be useful for storage cells)"},"jungfrau_use_gain_hg0":{"type":"boolean","default":false,"description":"Use high G0 (for low energy applications)"}}},"spot_finding_settings":{"type":"object","required":["enable","indexing","signal_to_noise_threshold","photon_count_threshold","max_pix_per_spot","min_pix_per_spot","high_resolution_limit_for_spot_count_low_res","ice_ring_width_q_recipA"],"properties":{"enable":{"type":"boolean","default":true,"description":"Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. \nEven if disabled spot finding information will still be send and written, though always with zero spots.\n"},"indexing":{"type":"boolean","default":true,"description":"Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.\n"},"signal_to_noise_threshold":{"type":"number","format":"float","minimum":0},"photon_count_threshold":{"type":"integer","format":"int64","minimum":0},"min_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"max_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"high_resolution_limit":{"type":"number","format":"float","description":"High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends\nas far as the detector reaches, i.e. the detection is not clipped in resolution.\n"},"low_resolution_limit":{"type":"number","format":"float","description":"Low resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding is not\nclipped at the low-resolution end. A value of 0 is accepted and means the same thing.\n"},"high_resolution_limit_for_spot_count_low_res":{"type":"number","format":"float","description":"High resolution threshold to consider spot \"low resolution\" [Angstrom]","minimum":2,"maximum":8},"quick_integration":{"type":"boolean","default":false,"deprecated":true,"description":"Ignored: accepted on input and always returned as false; will be removed in a future release.\nThe Lite and FPGA workflows index images but do not integrate them; integration is done by rugnux live.\n"},"ice_ring_width_q_recipA":{"type":"number","format":"float","minimum":0,"maximum":1,"default":0.03,"description":"Half-width of the ice ring band in q (1/A). Matches the offline default in image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online."},"high_res_gap_Q_recipA":{"type":"number","format":"float","minimum":0.1,"maximum":5,"default":1.5,"description":"This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.\nIf there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.\nThis option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.\n"},"adaptive_threshold":{"type":"boolean","default":false,"description":"Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring\nthreshold derived from each image's own noise, so the same setting works across datasets without\nper-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the\noperating point instead.\nUsed only on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).\nThe JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold;\nthere the setting is accepted and ignored, so the same settings can be shared across detectors.\n"},"false_pixels_per_frame":{"type":"number","format":"float","minimum":1,"maximum":100000,"default":100,"description":"Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.\nAbout 100 suits a multi-megapixel detector. 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This number will be lower than images expected if there were issues with data collection performance.\n"},"images_sent":{"type":"integer","format":"int64","description":"Images sent to the writer. \nThe value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.\n"},"images_written":{"type":"integer","format":"int64","description":"Images successfully written to disk.\nThe value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.\n"},"images_discarded_lossy_compression":{"type":"integer","format":"int64","description":"Images discarded by the lossy compression filter"},"max_image_number_sent":{"type":"integer","format":"int64"},"collection_efficiency":{"type":"number","format":"float","example":1,"minimum":0,"maximum":1},"compression_ratio":{"type":"number","format":"float","example":5.3,"minimum":0},"cancelled":{"type":"boolean"},"max_receiver_delay":{"type":"integer","format":"int64"},"indexing_rate":{"type":"number","format":"float"},"detector_width":{"type":"integer","format":"int64"},"detector_height":{"type":"integer","format":"int64"},"detector_pixel_depth":{"type":"integer","format":"int64","enum":[2,4]},"bkg_estimate":{"type":"number","format":"float"},"unit_cell":{"type":"string"},"error_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of error pixels on the detector"},"saturated_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of saturated pixels on the detector"},"roi_beam_pixels":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor number of valid pixels within this ROI\n"},"roi_beam_sum":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor sum of valid pixels within this ROI\n"}}},"fpga_status":{"type":"array","items":{"type":"object","required":["pci_dev_id","serial_number","base_mac_addr","eth_link_status","eth_link_count","eth_link_speed","power_usage_W","fpga_temp_C","hbm_temp_C","packets_sls","packets_udp","idle","fw_version","pcie_link_speed","pcie_link_width"],"properties":{"pci_dev_id":{"type":"string"},"serial_number":{"type":"string"},"fw_version":{"type":"string"},"base_mac_addr":{"type":"string"},"eth_link_count":{"type":"integer","format":"int64"},"eth_link_status":{"type":"integer","format":"int64"},"power_usage_W":{"type":"number","format":"float"},"fpga_temp_C":{"type":"number","format":"float"},"hbm_temp_C":{"type":"number","format":"float"},"packets_udp":{"type":"integer","format":"int64"},"packets_sls":{"type":"integer","format":"int64"},"idle":{"type":"boolean"},"pcie_link_speed":{"type":"integer","format":"int64","description":"PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)"},"pcie_link_width":{"type":"integer","format":"int64","description":"PCIe link width (expected value is 8 == x8)"}}}},"broker_status":{"type":"object","required":["state"],"properties":{"state":{"type":"string","enum":["Inactive","Idle","Busy","Measuring","Pedestal","Error"]},"progress":{"type":"number","format":"float","description":"Progress of data collection (only available if receiving is running)","example":1,"minimum":0,"maximum":1},"message":{"type":"string","description":"Message to display besides state of the jfjoch_broker; mostly used for errors and warnings\nThis matters especially for async functions (start/initialize), where API won't return reason\nfor the error during async operation.\n"},"message_severity":{"type":"string","enum":["success","info","warning","error"],"default":"error","description":"Level of the message to display"},"gpu_count":{"type":"integer","format":"int32","description":"Number of installed GPUs"},"broker_version":{"type":"string","description":"Version of the jfjoch_broker","example":"1.0.0-rc.128"}}},"image_pusher_status":{"type":"object","required":["pusher_type","addr","connected_writers"],"description":"Informs about status of the image pusher.\n","properties":{"pusher_type":{"$ref":"#/components/schemas/image_pusher_type"},"addr":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"List of addresses of image pushers.\nFor HDF5 socket - no addresses will be returned.\nFor ZeroMQ - list of addresses for each socket will be provided.\nFor TCP/IP - single address to connect all writers will be provided.\n"},"connected_writers":{"type":"integer","format":"int64","minimum":0,"description":"Number of connected writers \nFor ZeroMQ image socket: number is constant\nFor TCP/IP image socket: number is updated live during operation\n"},"images_written":{"type":"integer","format":"int64","minimum":0,"description":"Number of images written to the image socket.\nThis number is updated live during operation for TCP/IP image socket and direct HDF5 writer.\nIt is updated at the end of experiment for ZeroMQ image socket.\n"},"images_write_error":{"type":"integer","format":"int64","minimum":0,"description":"Number of images that could not be written to the image socket.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"},"writer_fifo_utilization":{"type":"array","items":{"type":"integer","format":"int64","minimum":0},"description":"Utilization of internal writer FIFO.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"}}},"plot":{"type":"object","required":["x","y","title"],"description":"x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly","properties":{"title":{"type":"string","default":""},"x":{"type":"array","items":{"type":"number","format":"float"}},"y":{"type":"array","items":{"type":"number","format":"float","nullable":true}},"z":{"type":"array","items":{"type":"number","format":"float","nullable":true}}}},"plot_unit_x":{"type":"string","enum":["image_number","q_recipA","d_A","angle_deg","ADU","grid_um"],"default":"image_number"},"plots":{"type":"object","required":["plot","unit_x"],"properties":{"title":{"type":"string"},"unit_x":{"$ref":"#/components/schemas/plot_unit_x"},"size_x":{"type":"number","format":"float","description":"Max X range of the plot"},"size_y":{"type":"number","format":"float","description":"Max Y range of the plot"},"plot":{"type":"array","items":{"$ref":"#/components/schemas/plot"}}}},"scan_result":{"type":"object","description":"Results of a scan","required":["images"],"properties":{"file_prefix":{"type":"string"},"rotation_unit_cell":{"$ref":"#/components/schemas/unit_cell"},"rotation_crystal_lattice":{"$ref":"#/components/schemas/crystal_lattice"},"rotation_bravais":{"type":"string","description":"Bravais lattice type of the global rotation-indexing solution: crystal-system\nletter + centering, e.g. \"tP\", \"oC\", \"cF\", \"hR\", \"mP\". Empty if not determined.\n"},"images":{"type":"array","items":{"type":"object","required":["efficiency","number"],"properties":{"efficiency":{"type":"number","format":"float"},"number":{"type":"integer","format":"int64","description":"Detector image number for a given cell"},"nx":{"type":"integer","format":"int64","description":"Cell position in X for grid scan"},"ny":{"type":"integer","format":"int64","description":"Cell position in Y for grid scan"},"angle":{"type":"number","format":"float","description":"Rotation angle associated with the image"},"bkg":{"type":"number","format":"float","description":"Background estimate"},"spindle_blind":{"type":"number","format":"float","description":"Fraction (0-1) of a rotation sweep's blind double cone that this orientation makes unrecoverable, assuming the nearest plausible lattice row is a lone 2-fold (a worst-case bound, not an estimate). At 0.5 and above a recovery protocol (second sweep, reorientation) should engage. Absent means the frame could not be assessed, which automation must treat the same as above threshold - it is not a zero.\n"},"spots":{"type":"integer","format":"int64","description":"Spot count"},"spots_low_res":{"type":"integer","format":"int64","description":"Spot count in low resolution range"},"spots_indexed":{"type":"integer","format":"int64","description":"Spot count within indexing tolerance"},"spots_ice":{"type":"integer","format":"int64","description":"Spot count within common ice ring resolutions"},"ice":{"type":"number","format":"float","description":"Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice)"},"index":{"type":"integer","format":"int64","description":"Indexing solution"},"latt_count":{"type":"integer","format":"int64","description":"Indexing lattice count"},"pr":{"type":"number","format":"float","description":"Profile radius, i.e. how far reflections are from the Ewald sphere"},"b":{"type":"number","format":"float","description":"B-Factor estimate"},"uc":{"$ref":"#/components/schemas/unit_cell"},"xfel_pulseid":{"type":"integer","format":"int64","description":"XFEL pulse ID"},"pixel_sum":{"type":"integer","format":"int64","description":"Total sum of all pixels"},"max":{"type":"integer","format":"int64","description":"Max viable pixel"},"sat":{"type":"integer","format":"int64","description":"Number of saturated pixels"},"err":{"type":"integer","format":"int64","description":"Number of error pixels"},"res":{"type":"number","format":"float","description":"Diffraction resolution estimate"}}}}}},"powder_calibration_fit_sigma":{"type":"object","description":"What the powder ring fit knows about its own answer, from the covariance of the converged\nproblem. Each sigma is in its parameter's own unit and is scaled by the residual scatter of\nthat fit, so it is the usual \"how far could this move before the fit got visibly worse\".\nThe two correlations are the ones that matter: a tilt and a beam-centre shift both displace a\nring's radius as cos(phi) and are told apart only by how that amplitude grows with the ring's\nradius, so as the rings run out the pair stops being separable and these approach 1.\nThe rotation sigmas and the correlations are absent when the tilt was not a free parameter.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI x [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI y [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Standard error of the fitted detector distance [mm]"},"poni_rot1_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot1 [rad]"},"poni_rot2_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot2 [rad]"},"correlation_beam_x_rot1":{"type":"number","format":"float","description":"Correlation between the fitted PONI x and rot1, -1 to 1"},"correlation_beam_y_rot2":{"type":"number","format":"float","description":"Correlation between the fitted PONI y and rot2, -1 to 1"}}},"powder_calibration_spot_check":{"type":"object","description":"Where the circle through the found spots puts the beam, and how far that is from the geometry\nactually fitted. An independent cross-check: it reads nothing from the file's own geometry, so\nit holds where the summed azimuthal profile does not - a profile binned about a badly wrong\ncentre shows each ring smeared across its sectors, and a fit on it converges on the wrong\nanswer without saying so. Two methods sharing no assumption, so the disagreement is the\nstatement. Absent when no spots were available.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Beam centre x the spots vote for [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Beam centre y the spots vote for [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Detector distance the spots imply [mm]"},"disagreement_pxl":{"type":"number","format":"float","description":"Distance between the spots' beam centre and the fitted one [pixels]"}}},"powder_calibration_quality":{"type":"object","description":"What a powder calibration knows about the geometry it produced. A calibration that has gone\nwrong - the wrong standard named, a header too far out for the rings to be found - looks\nexactly like one that has not until these are read.\n","properties":{"converged":{"type":"boolean","description":"Whether the geometry beside this is a measurement of the data at all. False means at least\none of its parameters was carried over from the input file rather than fitted - which looks\nexactly like a good fit in every other field here - and see not_converged_reason for which.\nrugnux --mode calibration writes no .poni file in that case, a PONI file having no field in\nwhich to say it, and exits non-zero.\n"},"not_converged_reason":{"type":"string","description":"What made converged false, in words. Absent when the calibration converged."},"calibrant":{"type":"string","description":"The powder standard the rings were fitted to, or the unit cell given in its place"},"method":{"type":"string","description":"How the rings were measured. rings fits the arcs of the run-summed (q x azimuth) azimuthal\nprofile; spots fits the pooled per-image spot lists.\n","enum":["rings","spots"]},"ring_points":{"type":"integer","format":"int64","description":"Ring measurements the fit used"},"rms_radial_pxl":{"type":"number","format":"float","description":"Scatter of those measurements about the fitted rings, as a radial distance [pixels]. The\nsingle number that separates a calibration that worked from one that did not.\n"},"beam_sigma_pxl":{"type":"number","format":"float","description":"Standard error the scatter implies on the beam centre [pixels], for a ring of that many\npoints. See powder_calibration_fit_sigma for what the fit itself says, which is not the same and\nis the larger of the two whenever the tilt is poorly separated.\n"},"direct_beam_x_pxl":{"type":"number","format":"float","description":"Where the direct beam lands [pixels]. NOT dataset_settings.beam_x_pxl, which is the PONI:\nthe two part company by distance*tan(tilt)/pixel as soon as the detector is tilted.\n"},"direct_beam_y_pxl":{"type":"number","format":"float","description":"Where the direct beam lands, y [pixels]"},"header_distance_mm":{"type":"number","format":"float","description":"The detector distance the input file declared, for comparison [mm]"},"ring_seed_distance_mm":{"type":"number","format":"float","description":"The distance measured from the ring radii before the fit ran [mm]. It is taken from the\nradii, the wavelength and the pixel size alone, so a large gap from header_distance_mm is\nthe answer to the question the calibration was run to ask. Absent when the profile showed\ntoo few rings to fix a scale.\n"},"tilt_refined":{"type":"boolean","description":"Whether the reported rot1/rot2 were measured by this fit. False means they were declined\nand pinned at the input file's values, because the rings could not separate a tilt from a\nshift of the beam centre.\n"},"tilt_significance":{"type":"number","format":"float","description":"How many of its own sigmas the fitted tilt stands from zero. Below about 3 it is not a\nmeasurement of a tilt but of a beam-centre shift, and the tilt is declined. Passing does\nnot certify a tilt: that estimator is limited by systematics rather than by this sigma.\n"},"fit_sigma":{"$ref":"#/components/schemas/powder_calibration_fit_sigma"},"spot_cross_check":{"$ref":"#/components/schemas/powder_calibration_spot_check"}}},"powder_calibration_output":{"type":"object","required":["dataset_settings"],"description":"The result of a powder-ring detector calibration - what rugnux --mode calibration writes as\n<prefix>.json, and what a calibration run over the image buffer would return.\n\ndataset_settings holds the geometry and nothing else, under the property names this API gives\nthem, so it can be POSTed or merged without translating a field. Its beam_x_pxl/beam_y_pxl is\nthe PONI, the foot of the perpendicular from the sample; where the beam actually lands is\ncalibration.direct_beam_x_pxl. The poni_rot*_rad are present whenever any of them is non-zero\nand absent when all are zero, since a body omitting them states a FLAT detector rather than an\nunstated one.\n","properties":{"dataset_settings":{"$ref":"#/components/schemas/dataset_settings"},"calibration":{"$ref":"#/components/schemas/powder_calibration_quality"},"jfjoch_version":{"type":"string","description":"Version of the program that produced this"}}},"calibration_statistics":{"type":"array","items":{"required":["module_number","storage_cell_number","pedestal_g0_mean","pedestal_g1_mean","pedestal_g2_mean","gain_g0_mean","gain_g1_mean","gain_g2_mean","masked_pixels"],"type":"object","properties":{"module_number":{"type":"integer","format":"int64"},"storage_cell_number":{"type":"integer","format":"int64"},"pedestal_g0_mean":{"type":"number","format":"float"},"pedestal_g1_mean":{"type":"number","format":"float"},"pedestal_g2_mean":{"type":"number","format":"float"},"gain_g0_mean":{"type":"number","format":"float"},"gain_g1_mean":{"type":"number","format":"float"},"gain_g2_mean":{"type":"number","format":"float"},"masked_pixels":{"type":"integer","format":"int64"}}}},"jfjoch_statistics":{"type":"object","description":"Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker","properties":{"detector":{"$ref":"#/components/schemas/detector_status"},"detector_list":{"$ref":"#/components/schemas/detector_list"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"image_format_settings":{"$ref":"#/components/schemas/image_format_settings"},"instrument_metadata":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer_settings":{"$ref":"#/components/schemas/file_writer_settings"},"data_processing_settings":{"$ref":"#/components/schemas/spot_finding_settings"},"measurement":{"$ref":"#/components/schemas/measurement_statistics"},"broker":{"$ref":"#/components/schemas/broker_status"},"fpga":{"$ref":"#/components/schemas/fpga_status"},"calibration":{"$ref":"#/components/schemas/calibration_statistics"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"},"pixel_mask":{"$ref":"#/components/schemas/pixel_mask_statistics"},"roi":{"$ref":"#/components/schemas/roi_definitions"},"az_int":{"$ref":"#/components/schemas/azim_int_settings"},"buffer":{"$ref":"#/components/schemas/image_buffer_status"},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"bragg_integration":{"$ref":"#/components/schemas/bragg_integration_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_status"}}},"error_message":{"type":"object","required":["msg","reason"],"properties":{"msg":{"type":"string","description":"Human readable message","example":"Detector in wrong state"},"reason":{"type":"string","description":"Enumerate field for automated analysis","enum":["WrongDAQState","Other"]}}},"roi_azimuthal":{"type":"object","description":"ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector","required":["name","q_min_recipA","q_max_recipA"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"q_min_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Minimum Q-range for the ROI"},"q_max_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Maximum Q-range for the ROI"},"phi_min_deg":{"type":"number","format":"float","description":"Lower azimuthal-angle bound of the sector [degrees]. 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Lattices outside given tolerance will be ignored"},"viable_cell_min_spots":{"type":"integer","format":"int64","minimum":5,"default":10,"description":"Minimum number of indexed spots required for a cell to be considered viable"},"index_ice_rings":{"type":"boolean","default":false,"description":"Include spots marked as ice rings in the indexing run. \nIf `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing.\n"},"rotation_indexing":{"type":"boolean","default":false,"deprecated":true,"description":"Ignored: accepted on input and always returned as false; will be removed in a future release.\nThe Lite and FPGA workflows index each image on its own, rotation or not; rotation indexing is done by rugnux live.\n"},"rotation_indexing_min_angular_range_deg":{"type":"number","format":"float","default":20,"minimum":1,"deprecated":true,"description":"Ignored, as `rotation_indexing`; always returned as 20.0."},"rotation_indexing_angular_stride_deg":{"type":"number","format":"float","default":0.5,"minimum":0,"deprecated":true,"description":"Ignored, as `rotation_indexing`; 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Same words in both:\n`x0`/`y0` is the image position of the module's readout pixel 0 and `fast_axis`/`slow_axis` say which\nway its fast and slow readout axes run in the image. With `mirror_y` on, a module's entry differs\nbetween the two by the mirror: for an image of height H, y0 (module_placement) = H - 1 - y0\n(custom_geometry), x0 is the same, and Yp and Yn swap in fast_axis/slow_axis. With `mirror_y` off they\nare equal.\n","required":["x0","y0","fast_axis","slow_axis"],"properties":{"x0":{"type":"number","description":"Image x of the module's readout pixel 0, before mirror_y"},"y0":{"type":"number","description":"Image y of the module's readout pixel 0, before mirror_y"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"}}},"detector_module_placement":{"type":"object","description":"One module of the image and where it lies on the detector plane, as rugnux measures it.\nFrame: `custom_geometry` is BEFORE `mirror_y` (the image as assembled from the readout); `module_placement`\nis AFTER `mirror_y` (the image as stored, the only one a file reader sees). Same words in both:\n`x0`/`y0` is the image position of the module's readout pixel 0 and `fast_axis`/`slow_axis` say which\nway its fast and slow readout axes run in the image. With `mirror_y` on, a module's entry differs\nbetween the two by the mirror: for an image of height H, y0 (module_placement) = H - 1 - y0\n(custom_geometry), x0 is the same, and Yp and Yn swap in fast_axis/slow_axis. With `mirror_y` off they\nare equal.\n`x0`, `y0`, `fast_axis` and `slow_axis` identify the module, whatever the order of the entries, and with\nthe module size they give its box in the image. The plane is in image pixels (a pixel's centre at its\nindex): readout pixel (i, j) - i along the fast axis, j along the slow axis from pixel 0 - lies on it at\n(x0_plane, y0_plane) + i fast_step + j slow_step.\nAs assembled: x0_plane = x0, y0_plane = y0, and each step is the unit vector of its axis\n(Xp = [1, 0], Xn = [-1, 0], Yp = [0, 1], Yn = [0, -1]).\n","required":["x0","y0","fast_axis","slow_axis","x0_plane","y0_plane","fast_step","slow_step"],"properties":{"x0":{"type":"integer","format":"int64","minimum":0,"description":"Image x of the module's readout pixel 0, after mirror_y"},"y0":{"type":"integer","format":"int64","minimum":0,"description":"Image y of the module's readout pixel 0, after mirror_y"},"fast_axis":{"$ref":"#/components/schemas/detector_module_direction"},"slow_axis":{"$ref":"#/components/schemas/detector_module_direction"},"x0_plane":{"type":"number","description":"Plane x of readout pixel 0, in image pixels"},"y0_plane":{"type":"number","description":"Plane y of readout pixel 0, in image pixels"},"fast_step":{"type":"array","items":{"type":"number"},"minItems":2,"maxItems":2,"description":"Plane displacement (x, y) for one pixel along the fast readout axis"},"slow_step":{"type":"array","items":{"type":"number"},"minItems":2,"maxItems":2,"description":"Plane displacement (x, y) for one pixel along the slow readout axis"}}},"detector":{"type":"object","required":["description"],"properties":{"description":{"type":"string","minLength":1},"serial_number":{"type":"string","default":"Unknown","minLength":1},"type":{"$ref":"#/components/schemas/detector_type"},"high_voltage_V":{"type":"integer","format":"int64","minimum":0,"maximum":200,"default":0},"udp_interface_count":{"type":"integer","format":"int64","minimum":1,"maximum":2,"default":1},"module_sync":{"type":"boolean","default":true,"description":"Use module 0 as master for timing. 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The cost grows as the cube\n(2n+1)^3 of candidates per image, which is why online keeps a fixed, predictable value\ninstead of taking it from whichever crystal is mounted.\n\nOmitting the field selects the default above; it is never interpreted as \"choose per\ncrystal\". The offline tools (rugnux, viewer) do derive it from the refined cell when it is\nleft unset there, but that is their own default and is not reachable through this API.\n"}}},"jfjoch_settings":{"type":"object","required":["detector","frontend_directory","image_pusher"],"description":"Default settings for Jungfraujoch software. \nThis structure is used to provide default settings using configuration JSON file and is not used in HTTP.\n","properties":{"pcie":{"$ref":"#/components/schemas/pcie_devices"},"zeromq":{"$ref":"#/components/schemas/zeromq_settings"},"tcp":{"$ref":"#/components/schemas/tcp_settings"},"instrument":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer":{"$ref":"#/components/schemas/file_writer_settings"},"detector":{"type":"array","minItems":1,"items":{"$ref":"#/components/schemas/detector"}},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"bragg_integration":{"$ref":"#/components/schemas/bragg_integration_settings"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"azim_int":{"$ref":"#/components/schemas/azim_int_settings"},"image_format":{"$ref":"#/components/schemas/image_format_settings"},"image_buffer_MiB":{"type":"integer","minimum":128,"default":2048,"description":"Size of internal buffer in MiB for images before they are sent to a stream"},"verbose":{"type":"boolean","default":false,"description":"Print extra debug information"},"receiver_threads":{"type":"integer","minimum":1,"maximum":512,"default":64,"description":"Number of threads used by the receiver"},"numa_policy":{"type":"string","deprecated":true,"description":"Ignored value"},"frontend_directory":{"type":"string","description":"Location of built JavaScript web frontend"},"spot_finding":{"$ref":"#/components/schemas/spot_finding_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_type"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"},"rugnux":{"$ref":"#/components/schemas/rugnux_settings"}}},"rugnux_settings":{"type":"object","description":"Rugnux live mode: rotation collections from a DECTRIS detector are processed by rugnux\ninside the broker while they arrive, and the merged result is sent to the writer. Serial\ncollections, from a DECTRIS detector or converted by the FPGA (JUNGFRAU), are analysed on the GPU\nafter a pre-pass on their first images that decides the beam centre, distance and mask (`stills` in\n`/rugnux/status`), and merged as they go.\n","properties":{"enable":{"type":"boolean","default":false,"description":"Process DECTRIS rotation collections with rugnux live, and serial collections on the GPU after a pre-pass"},"reserved_cpus":{"type":"integer","format":"int64","minimum":0,"default":4,"description":"CPU threads left to the receiver and the image pusher while rugnux runs"},"deadline_s":{"type":"number","format":"double","minimum":0,"default":60,"description":"Fixed cutoff: this long after the last image the analysis is cut, and the collection ends\nwith what it has established (as `POST /cancel` after the last image does). 0 means no cutoff.\n"}}},"rugnux_status":{"type":"object","required":["enable","reserved_cpus","model_loaded"],"properties":{"enable":{"type":"boolean","description":"Rugnux live mode is enabled"},"reserved_cpus":{"type":"integer","format":"int64","description":"CPU threads left to the receiver and the image pusher while rugnux runs"},"deadline_s":{"type":"number","format":"double","description":"Seconds after the last image at which the analysis is cut; 0 means no cutoff"},"model_loaded":{"type":"boolean","description":"A model was uploaded with `PUT /config/rugnux/model`"},"model_size_bytes":{"type":"integer","format":"int64","description":"Size of the uploaded model file"}}},"rugnux_live_step":{"type":"object","required":["title","started_s","notes"],"properties":{"title":{"type":"string"},"started_s":{"type":"number","format":"double","description":"Start of the step, since the first image (negative if before it)"},"duration_s":{"type":"number","format":"double","description":"Set once the next step starts or the run ends"},"notes":{"type":"array","description":"What the step found (e.g. lattice, space group)","items":{"type":"string"}}}},"rugnux_summary_row":{"type":"object","required":["label","value"],"properties":{"label":{"type":"string"},"value":{"type":"string"}}},"rugnux_triage_item":{"type":"object","description":"A line of the pathology checklist of `_report.txt` (its SUMMARY), in the report's words.\n`ok`: looked for and not found; `attention`: its warning fired (its codes are in the report's\nPATHOLOGY_FLAGS); `serious`: a pathology that leaves no result to use - no lattice, or a merge without\nsignal (the report's verdict FAILED or UNUSABLE); `not_measured`: it could not be looked for on this run.\n","required":["label","codes","severity","text"],"properties":{"label":{"type":"string","description":"Name of the condition, e.g. \"Twinning\" - the summary row's label"},"codes":{"type":"array","description":"The PATHOLOGY_FLAGS codes the line stands for, e.g. TWINNING","items":{"type":"string"}},"severity":{"type":"string","enum":["ok","attention","serious","not_measured"]},"text":{"type":"string","description":"The summary row's own words; empty where it has none"},"detail":{"type":"string","description":"The report's warnings that fired for it, one per line; absent where none fired"}}},"rugnux_live_model":{"type":"object","description":"What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The\nR-factors here are those of the placed model with its own coordinates and B factors; what refinement made\nof it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by\nmolecular replacement.\n","required":["placement","model_name","predicted","reason","mr_decision","mr_space_group","anomalous_site"],"properties":{"placement":{"type":"string","description":"RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED"},"model_name":{"type":"string"},"predicted":{"type":"boolean","description":"Searched for as a predicted model"},"reason":{"type":"string","description":"Why the model could not be searched for or validated; empty otherwise"},"r_work":{"type":"number","format":"double"},"r_free":{"type":"number","format":"double"},"cc_model":{"type":"number","format":"double","description":"Correlation of the merged intensities with the placed model's, over all reflections"},"fit_sigma":{"type":"number","format":"double","description":"How far R-work stands below that of the same model in random orientations, in standard deviations"},"map_atom_sigma":{"type":"number","format":"double","description":"Mean 2mFo-DFc value at the atom centres, in map sigma"},"rigid_body_angle_deg":{"type":"number","format":"double"},"rigid_body_shift_A":{"type":"number","format":"double"},"mr_decision":{"type":"string","description":"Molecular replacement's decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run"},"mr_space_group":{"type":"string","description":"The group molecular replacement placed the model in; empty where it placed none"},"copies":{"type":"integer","format":"int64","description":"Copies placed by molecular replacement"},"tf_z":{"type":"number","format":"double","description":"Translation-function Z-score, the highest of the copies'"},"rf_z":{"type":"number","format":"double","description":"Rotation-function Z-score of the first copy's orientation"},"llg_z":{"type":"number","format":"double","description":"Likelihood Z-score after the rigid body, where a copy's translation function did not stand out"},"mr_d_min":{"type":"number","format":"double","description":"High-resolution limit of the molecular-replacement search, in Angstrom"},"anomalous_site":{"type":"string","description":"Atom with the strongest anomalous difference density, e.g. \"SG CYS A7\"; empty where there is no anomalous map"},"anomalous_site_sigma":{"type":"number","format":"double","description":"Anomalous difference density at that atom, in map sigma"},"refinement":{"$ref":"#/components/schemas/rugnux_live_refinement"}}},"rugnux_live_refinement":{"type":"object","description":"The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set\nwhere a placed model was refined or its refinement failed; absent where the model was not placed or\nrefinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline\nor cancel can cut it.\n","required":["performed","cancelled","reason","on_gpu","seconds","blob_count","blobs"],"properties":{"performed":{"type":"boolean","description":"Refinement ran; false with `reason` where it failed"},"cancelled":{"type":"boolean","description":"The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the\nrest left out (cut before the first, the model is the placement's)\n"},"reason":{"type":"string","description":"Why refinement did not run to the end; empty otherwise"},"on_gpu":{"type":"boolean"},"seconds":{"type":"number","format":"double","description":"Wall time of the refinement"},"r_work":{"type":"number","format":"double","description":"R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)"},"r_free":{"type":"number","format":"double","description":"R-free of the refined model, on the same reflections as `r_work`"},"rmsd_bonds_A":{"type":"number","format":"double","description":"RMS deviation of the bond lengths from the dictionary, where the restrained stage ran"},"rmsd_angles_deg":{"type":"number","format":"double","description":"RMS deviation of the bond angles from the dictionary, where the restrained stage ran"},"blob_count":{"type":"integer","format":"int64","description":"Unexplained blobs of the refined model's mFo-DFc map (above 3 sigma, peaking above 4)"},"blobs":{"type":"array","description":"The strongest blobs, at most 50, strongest first","items":{"$ref":"#/components/schemas/rugnux_live_blob"}}}},"rugnux_live_blob":{"type":"object","description":"A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on\nwhat is measured, to point a person at the density - not an identification.\n","required":["kind","x","y","z","peak_sigma","volume_A3","nearest_atom"],"properties":{"kind":{"type":"string","enum":["WATER","ION","LIGAND","MODEL_ERROR","UNASSIGNED"]},"x":{"type":"number","format":"double","description":"Centroid, Cartesian Angstrom, in the frame of the refined model (`/rugnux/model.cif`)"},"y":{"type":"number","format":"double"},"z":{"type":"number","format":"double"},"peak_sigma":{"type":"number","format":"double","description":"The highest point, in map sigma"},"volume_A3":{"type":"number","format":"double","description":"Volume above 3 sigma, in cubic Angstrom"},"nearest_atom":{"type":"string","description":"e.g. \"OG1 THR A42\""},"nearest_atom_distance_A":{"type":"number","format":"double","description":"Absent where no atom is within 12 Angstrom"}}},"rugnux_live_stills":{"type":"object","description":"Serial frames analysed on the GPU: the pre-pass on the first images (the beam\ncentre, distance and mask the whole collection is analysed with), and the analysis since.\n","required":["prepass","images_held","images_needed","file_beam_x_pxl","file_beam_y_pxl","file_distance_mm","images_analysed","images_indexed"],"properties":{"prepass":{"type":"string","enum":["Holding","Running","Done","Failed"],"description":"Holding the first images, running on them, or done (Failed - the stated geometry and mask are used)"},"images_held":{"type":"integer","format":"int64","description":"Images held for the pre-pass"},"images_needed":{"type":"integer","format":"int64","description":"Images the pre-pass runs on"},"prepass_s":{"type":"number","format":"double","description":"How long the pre-pass took"},"file_beam_x_pxl":{"type":"number","format":"double"},"file_beam_y_pxl":{"type":"number","format":"double"},"file_distance_mm":{"type":"number","format":"double"},"beam_x_pxl":{"type":"number","format":"double","description":"Beam centre the pre-pass decided (where the beam lands)"},"beam_y_pxl":{"type":"number","format":"double"},"distance_mm":{"type":"number","format":"double","description":"Detector distance the pre-pass decided"},"shadow_pixels":{"type":"integer","format":"int64","description":"Pixels masked as the beam-stop shadow"},"bad_pixels":{"type":"integer","format":"int64","description":"Pixels masked as defective (hot, dead, error value)"},"images_analysed":{"type":"integer","format":"int64"},"images_indexed":{"type":"integer","format":"int64"},"analysis_rate_hz":{"type":"number","format":"double","description":"Images analysed per second since the pre-pass"}}},"rugnux_live_shell":{"type":"object","description":"A resolution shell of the merge: a row of the shell table of `_report.txt`, with R_split from its serial\nstatistics and R-free from its MODEL VALIDATION, on the same shells. Fractions, not percent. A quantity\nnot measured for this shell or this run is absent.\n","required":["d_min","d_max","n_obs","n_unique"],"properties":{"d_min":{"type":"number","format":"double","description":"High-resolution limit of the shell, in Angstrom (the row label of the report's table)"},"d_max":{"type":"number","format":"double","description":"Low-resolution limit of the shell, in Angstrom"},"n_obs":{"type":"integer","format":"int64","description":"Observations merged"},"n_unique":{"type":"integer","format":"int64","description":"Unique reflections"},"completeness":{"type":"number","format":"double"},"multiplicity":{"type":"number","format":"double"},"i_over_sigma":{"type":"number","format":"double","description":"Mean I/sigma(I) of the merged reflections"},"r_meas":{"type":"number","format":"double","description":"Rotation only, as in the report"},"cc_half":{"type":"number","format":"double","description":"CC1/2 of the shell table"},"cc_ref":{"type":"number","format":"double","description":"CC against the reference data, where reference data were given"},"r_split":{"type":"number","format":"double","description":"Serial data only, with every frame whole in one half-set"},"r_free":{"type":"number","format":"double","description":"R-free of the placed model (as given, not refined) over the shell's free reflections. In `overall`, the\nR-free of the model the run ended with: the refined model's (`model.refinement.r_free`) where rugnux\nrefined it, else the placed model's (`model.r_free`).\n"}}},"rugnux_live_frame_range":{"type":"object","description":"A stretch of a rotation sweep the merge did not take at face value: downgraded (merged at the reduced\nweight its own scale and sigmas give it) or rejected (nothing of it reached the merge), with the\nreason the sweep-quality diagnostic saw - the lines of the report's SWEEP section.\n","required":["first_image","last_image","disposition","reason"],"properties":{"first_image":{"type":"integer","format":"int64","description":"First image of the stretch, inclusive, numbered as the collection's images"},"last_image":{"type":"integer","format":"int64","description":"Last image of the stretch, inclusive"},"disposition":{"type":"string","enum":["downgraded","rejected"]},"reason":{"type":"string","description":"What was seen over the stretch, e.g. \"out of beam\", \"no diffraction\", \"radiation damage\""}}},"rugnux_live_status":{"type":"object","description":"Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`.\nTimes are taken when the image puller received a message, and are in seconds since the first image\n(before it arrives, since now). The frame rate is `(images_received - 1) / last_image_s`.\n","required":["state","message","images_expected","images_received","elapsed_s","steps","verdict","verdict_text","summary","warnings","probe","placed_model","refined_model","anomalous_map","anomalous_signal"],"properties":{"state":{"type":"string","enum":["Idle","Running","Done","Failed","Cancelled","Skipped"]},"placed_model":{"type":"boolean","description":"The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from\n`/rugnux/map.ccp4`.\n"},"refined_model":{"type":"boolean","description":"The run refined the placed model: `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and\nits maps unless asked for `stage=placed`.\n"},"anomalous_map":{"type":"boolean","description":"The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map\n(`/rugnux/map.ccp4?type=anom`).\n"},"anomalous_signal":{"type":"boolean","description":"The merged data carry usable anomalous signal (the summary's \"Anomalous\" row says so)"},"model":{"$ref":"#/components/schemas/rugnux_live_model"},"stills":{"$ref":"#/components/schemas/rugnux_live_stills"},"shells_merge":{"type":"string","description":"Which merge `shells` are of - \"the collection\", or on serial data a provisional merge such as\n\"50% of the images (provisional)\"; absent until there is a merge\n"},"shells":{"type":"array","description":"Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of\n`_report.txt`. Rotation: once the run is over; serial: at each provisional merge and at the end.\n`overall` is the same table's \"Overall\" row (whole-merge completeness, multiplicity, I/sigma, CC1/2,\nR_meas or R_split, CCref, and the R-free of the final model - refined where rugnux refined it, as\n`model.refinement.r_free`, else as placed, as `model.r_free`), present with `shells`.\n","items":{"$ref":"#/components/schemas/rugnux_live_shell"}},"overall":{"$ref":"#/components/schemas/rugnux_live_shell"},"frame_scales":{"type":"array","description":"Rotation, once the run is over: the per-image scale factor of the merge, one entry per image of the\ncollection in its order, 0 where the image got none (not indexed, or rejected). Absent on serial\ndata and until there is a merge.\n","items":{"type":"number","format":"float"}},"frame_ranges":{"type":"array","description":"Rotation, once the run is over: the stretches of the sweep the merge downgraded or rejected, in\norder; every image outside them is merged at its own weight. Absent on serial data and until there\nis a merge; empty where the whole sweep was merged.\n","items":{"$ref":"#/components/schemas/rugnux_live_frame_range"}},"space_group":{"type":"string","description":"Space group of the result (the summary's \"Space group\" row); absent until the run is over"},"d_min":{"type":"number","format":"double","description":"High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge"},"isa":{"type":"number","format":"double","description":"ISa of the error model; absent until the run is over, or where it was not determined"},"probe":{"type":"string","description":"Answer of the early lattice probe on the first 60 degrees; empty until it answers, and the run's own lattice once the run has indexed"},"probe_s":{"type":"number","format":"double","description":"When the probe answered (or the run indexed), since the first image"},"start_to_first_image_s":{"type":"number","format":"double","description":"From the START message to the first image; set once the first image arrives"},"message":{"type":"string","description":"Why the run failed or was skipped"},"images_expected":{"type":"integer","format":"int64"},"expected_collection_s":{"type":"number","format":"double","description":"How long the collection is set up to take - images_expected times the image time; absent if not known"},"images_received":{"type":"integer","format":"int64"},"elapsed_s":{"type":"number","format":"double"},"step_progress":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"Fraction of the current pass's images"},"steps":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_live_step"}},"last_image_s":{"type":"number","format":"double","description":"When the last image arrived, since the first image; set once the collection is over"},"cut":{"type":"string","description":"Empty, or why the analysis was cut: `deadline` (`deadline_s` after the last image) or `cancel`\n(`POST /cancel`). The end message then carried what was established at the cut.\n"},"cut_s":{"type":"number","format":"double","description":"When the analysis was cut, since the first image"},"last_image_to_written_s":{"type":"number","format":"double","description":"From the last image received to all results written"},"verdict":{"type":"string","description":"OK, WARNINGS, UNUSABLE, FAILED or CANCELLED; empty until the run is over"},"verdict_text":{"type":"string"},"summary":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_summary_row"}},"warnings":{"type":"array","items":{"type":"string"}},"triage":{"type":"array","description":"The pathology checklist of the report, in its order. Rotation: once the run is over; serial: at each\nprovisional merge and at the end. Absent until there is one.\n","items":{"$ref":"#/components/schemas/rugnux_triage_item"}}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\nIt also clears the image buffer, the previous collection's plots and live rugnux status, disables live rugnux analysis and removes the rugnux model.\nIt drops the previous dataset's bearer tokens and resets its settings, so nothing of that dataset stays readable.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\nOptional `tokens` protect the dataset: while set, its statistics, buffered images and plots\nrequire `Authorization: Bearer <token>`.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately.\nThe operation that finished either succeeded, was cancelled, or ended with a warning.\n"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code, or the operation that finished ended in an error -\nmissing packets, or a writer that could not write - see output message.\nA cancelled data collection is not an error.\n","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nWith rugnux live mode (`/config/rugnux`) the command also cuts the rugnux analysis, during the collection\nor after its last image alike: the collection ends with what the analysis has established\n(see `cut` in `/rugnux/status`). After the last image the collection itself is complete and is not\nmarked as cancelled.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/bragg_integration":{"put":{"summary":"Change Bragg integration settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get Bragg integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/rugnux":{"put":{"summary":"Change rugnux live mode settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get rugnux live mode settings and model status","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_status"}}}}}}},"/config/rugnux/model":{"put":{"summary":"Upload the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\nThe model (PDB or mmCIF, optionally gzipped; at most 64 MiB) is used for molecular replacement\nand validation of every following rugnux live collection, until it is removed with\n`DELETE /config/rugnux/model` or replaced by another upload.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Empty body, or not a model that can be read (PDB or mmCIF, optionally gzipped)"},"413":{"description":"Model larger than 64 MiB"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"delete":{"summary":"Remove the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/rugnux/status":{"get":{"summary":"Get live rugnux processing status of the last collection","description":"Can be done anytime","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_live_status"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/rugnux/model.cif":{"get":{"summary":"Get the model as placed by the last rugnux live run","description":"The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the\n`_model.cif` file written beside the data: the data's cell and space group, with the input model's own\nmetadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.\nWhere the run refined the model, the refined model unless asked for `stage=placed`.\n","parameters":[{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model, or (`stage=refined`) refined none"}}}},"/rugnux/map.ccp4":{"get":{"summary":"Get an electron-density map of the last rugnux live run","description":"The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map\ncoefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where\nthe model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and\nRMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run\nrefined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;\nthe anomalous map stays on the placed model's phases.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc","anom"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map,\n(F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map`\nin `/rugnux/status`)\n"},{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type or stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs, or (`stage=refined`) refined none"}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","description":"`measurement` is omitted unless the request carries a valid bearer token for a protected\ndataset (see `tokens` in `/start`).\n","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection (dataset name, unit cell, ...)","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in binary format (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector (binary)","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as binary array (4-byte; unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Mask is not 4-byte unsigned integer array or empty body"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/mask.tiff":{"get":{"summary":"Get mask of the detector (TIFF)","description":"Should be in `Idle` state.\nGet full pixel mask of the detector\nSee NXmx standard for meaning of pixel values\n","responses":{"200":{"description":"Pixel mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask.tiff":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (TIFF)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked","responses":{"200":{"description":"User mask in TIFF format (4 byte; unsigned)","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}}}},"put":{"summary":"Upload user mask of the detector","description":"Should be in `Idle` state.\nUpload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.\nIf detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.\nIn the latter case - module gaps are ignored and don't need to be assigned value.\nMask is expected as a single-channel TIFF (8-, 16- or 32-bit integer, signed or unsigned).\n0 - good pixel, other value - masked\nUser mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.\nUser mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.\n","requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Not a valid single-channel TIFF or size doesn't match the detector"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/preview/pedestal.tiff":{"get":{"parameters":[{"in":"query","name":"gain_level","required":true,"schema":{"type":"integer"},"description":"Gain level (0, 1, 2)"},{"in":"query","name":"sc","schema":{"type":"integer"},"description":"Storage cell number"}],"summary":"Get pedestal in TIFF format","responses":{"200":{"description":"Calibration image","content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Invalid gain level or storage cell number"},"404":{"description":"No calibration recorded so far"}}}},"/preview/plot":{"get":{"summary":"Generate 1D plot from Jungfraujoch","parameters":[{"$ref":"#/components/parameters/binning"},{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/fill_value"},{"$ref":"#/components/parameters/experimental_coord"},{"$ref":"#/components/parameters/azint_unit"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/plots"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/preview/plot.bin":{"get":{"summary":"Generate 1D plot from Jungfraujoch and send in raw binary format.\nData are provided as (32-bit) float binary array.\nThis format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.\n","parameters":[{"$ref":"#/components/parameters/plot_type"},{"$ref":"#/components/parameters/roi"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/result/scan":{"get":{"summary":"Get full scan result","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/scan_result"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No grid scan recorded"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/start.cbor":{"get":{"summary":"Get Start message in CBOR format","description":"Contains metadata for a dataset (e.g., experimental geometry)","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Return start message","content":{"application/cbor":{"schema":{"type":"string","format":"binary"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No measurement so far"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/live/events":{"get":{"summary":"Event stream of the collection, for a reader following it","description":"Server-sent events (text/event-stream) for the current collection, from the moment /start has\naccepted it: first its whole history, then every change, until it ends or a new collection\nbegins. Only one reader at a time. Events, each with a JSON `data` line:\n- `start` {run_number, run_name, file_prefix, number_of_images, images_per_file, cbor} - first,\n  once the start message is known: at once for a JUNGFRAU, when the detector sends its own for\n  a DECTRIS. `cbor` is the start message the writer of the master file received, CBOR in base64;\n  a reader builds the dataset from it;\n- `file` {file_number, file, first_image, image_count} - a data file closed and renamed into\n  place; `file` is relative to the collection's root, as the writer named it;\n- `end` {images, error?} - every writer acknowledged the end: the data files and the master\n  file are in place; `images` is the number of images collected. Also sent, with `error`, when\n  the measurement ends any other way - before the start message, for one. The stream then closes;\n- `superseded` {run_number} - a new collection began. The stream then closes.\nA comment line (`: keepalive`) every 10 s when nothing happens.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Event stream","content":{"text/event-stream":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No collection has started"},"409":{"description":"Another reader is following the collection, or the image pusher does not report closed data files"}}}},"/image_buffer/image.cbor":{"get":{"summary":"Get image message in CBOR format","description":"Contains full image data and metadata. 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Can be only run when Jungfraujoch is not collecting data.","responses":{"200":{"description":"Done"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/image_buffer/status":{"get":{"summary":"Get status of the image buffers","description":"Can be run at any stage of Jungfraujoch operation, including during data collection.\nThe status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots,\nthen image might be replaced in the buffer between calling /images and /image.cbor.\n","responses":{"200":{"description":"Done","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_buffer_status"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/version":{"get":{"summary":"Get Jungfraujoch version of jfjoch_broker","responses":{"200":{"description":"Release number of 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       var container = document.getElementById('redoc');
       Redoc.hydrate(__redoc_state, container);
diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index 7f25b8d7b..53b50509f 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -552,6 +552,8 @@ struct EndMessage {
     std::optional<PlacedModelMessage> refined_model;
     std::optional<MtzTable> refined_map_coefficients;
     std::optional<DensityBlobsMessage> blobs;
+    // And the run's results report, for <file_prefix>_report.txt: the text `rugnux` writes (rugnux/ResultReport.h).
+    std::optional<std::string> report;
 };
 
 struct MetadataMessage {
diff --git a/docs/CBOR.md b/docs/CBOR.md
index ccee96418..29f54265b 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -331,6 +331,7 @@ Every scalar of the image message is optional: a quantity that was not computed
 | refined_model                    | object (optional)        | The placed model after refinement, written as `<file_prefix>_refined_model.cif` and `<file_prefix>_refined_model.pdb`; same layout as `placed_model` | |
 | refined_map_coefficients         | object (optional)        | Map coefficients of the refined model, written as `<file_prefix>_refined_maps.mtz`. An MTZ table (layout below) | |
 | blobs                            | object (optional)        | Unexplained blobs of the refined model's mFo-DFc map, strongest first, written as `<file_prefix>_blobs.json`. One array per field, one entry per blob: `kind` (Array(string): `WATER`, `ION`, `LIGAND`, `MODEL_ERROR`, `UNASSIGNED`), `x`, `y`, `z` (double, centroid, Angstrom), `peak_sigma` (double, map rms), `volume` (double, Angstrom^3), `score` (double, sigma Angstrom^3), `nearest_atom` (Array(string)), `nearest_atom_distance` (double, Angstrom), `polar_contacts`, `metal_contacts` (int32), `anomalous_sigma` (double, 0 where there is no anomalous map) | |
+| report                           | string (optional)        | The in-broker analysis run's results report, written as `<file_prefix>_report.txt`: the text `rugnux` writes as its own `_report.txt` (see [RUGNUX_REPORT](RUGNUX_REPORT.md)) | |
 
 End-message vector fields are optional. When present, they provide master-file summary data so readers can inspect scan-level and per-image analysis results without opening every linked data file. Missing optional per-image values are encoded by the producer as zero unless otherwise noted.
 
diff --git a/docs/JFJOCH_BROKER.md b/docs/JFJOCH_BROKER.md
index 7a0ddb37a..1909e9d19 100644
--- a/docs/JFJOCH_BROKER.md
+++ b/docs/JFJOCH_BROKER.md
@@ -255,7 +255,8 @@ The results - the merged data, the map coefficients and, with a model, the place
 refinement - travel to the writer in the end message, which writes them beside the master file as
 `<file_prefix>.mtz`, `<file_prefix>_maps.mtz`, `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`,
 and `<file_prefix>_refined_model.cif` (and `.pdb`), `<file_prefix>_refined_maps.mtz` and
-`<file_prefix>_blobs.json`, as rugnux names them. These files name both programs as the software that
+`<file_prefix>_blobs.json`, as rugnux names them, and the results report `<file_prefix>_report.txt` - the
+report `rugnux` writes for its runs. These files name both programs as the software that
 made them: the MTZ files in a HISTORY record beside Rugnux's, the models in their `_software` loop
 (Rugnux, and Jungfraujoch for the data collection). An end message
 that would be too large for the pushers' buffer (256 MiB) goes without them, with an error in the log
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index be0bba48e..96bf1cc40 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -12,8 +12,11 @@ namespace {
         if (!cbor_value_is_text_string(&value))
             throw JFJochException(JFJochExceptionCategory::CBORError, "String expected");
 
-        std::vector<char> s(16384);
-        size_t len = s.size() - 1;
+        // As long as the string is: a model's metadata or a results report runs to tens of kB
+        size_t len;
+        cborErr(cbor_value_calculate_string_length(&value, &len));
+        std::vector<char> s(len + 1);
+        len = s.size();
         cborErr(cbor_value_copy_text_string(&value, s.data(), &len, nullptr));
         s[len] = 0;
         cborErr(cbor_value_advance(&value));
@@ -1823,6 +1826,8 @@ namespace {
                 message.refined_map_coefficients = ProcessMtzTableElement(value);
             else if (key == "blobs")
                 message.blobs = ProcessDensityBlobsElement(value);
+            else if (key == "report")
+                message.report = GetCBORString(value);
             else if (key == "rotation_lattice") {
                 std::vector<float> tmp;
                 GetCBORFloatArray(value, tmp);
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index 4f7bdb8cb..8c37bc970 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -1004,6 +1004,7 @@ void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
     CBOR_ENC(mapEncoder, "refined_model", message.refined_model);
     CBOR_ENC(mapEncoder, "refined_map_coefficients", message.refined_map_coefficients);
     CBOR_ENC(mapEncoder, "blobs", message.blobs);
+    CBOR_ENC(mapEncoder, "report", message.report);
 
     cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
 
diff --git a/frontend/src/client/types.gen.ts b/frontend/src/client/types.gen.ts
index b38f09f9c..4fec9d300 100644
--- a/frontend/src/client/types.gen.ts
+++ b/frontend/src/client/types.gen.ts
@@ -386,7 +386,10 @@ export type dataset_settings = {
      */
     max_spot_count?: number;
     /**
-     * Flag spots as ice rings and reduce their effect on indexing
+     * Flag spots as ice rings and reduce their effect on indexing. Left out, the broker's own
+     * spot finding treats no spot as an ice ring, rugnux live decides as a bare `rugnux` would (on
+     * for a rotation sweep, off for stills), and the master file carries no `detect_ice_rings`.
+     *
      */
     detect_ice_rings?: boolean;
     /**
@@ -2356,7 +2359,10 @@ export type rugnux_live_shell = {
      */
     r_split?: number;
     /**
-     * R-free of the placed model (as given, not refined) over the shell's free reflections
+     * R-free of the placed model (as given, not refined) over the shell's free reflections. In `overall`, the
+     * R-free of the model the run ended with: the refined model's (`model.refinement.r_free`) where rugnux
+     * refined it, else the placed model's (`model.r_free`).
+     *
      */
     r_free?: number;
 };
@@ -2425,7 +2431,8 @@ export type rugnux_live_status = {
      * Merging statistics by resolution shell of the latest merge, coarse to fine, as the shell table of
      * `_report.txt`. Rotation: once the run is over; serial: at each provisional merge and at the end.
      * `overall` is the same table's "Overall" row (whole-merge completeness, multiplicity, I/sigma, CC1/2,
-     * R_meas or R_split, CCref, and the overall R-free of the model validated on it), present with `shells`.
+     * R_meas or R_split, CCref, and the R-free of the final model - refined where rugnux refined it, as
+     * `model.refinement.r_free`, else as placed, as `model.r_free`), present with `shells`.
      *
      */
     shells?: Array<rugnux_live_shell>;
@@ -2457,11 +2464,11 @@ export type rugnux_live_status = {
      */
     isa?: number;
     /**
-     * Answer of the early lattice probe on the first 60 degrees; empty until it answers
+     * Answer of the early lattice probe on the first 60 degrees; empty until it answers, and the run's own lattice once the run has indexed
      */
     probe: string;
     /**
-     * When the probe answered, since the first image
+     * When the probe answered (or the run indexed), since the first image
      */
     probe_s?: number;
     /**
@@ -2795,7 +2802,10 @@ export type dataset_settingsWritable = {
      */
     max_spot_count?: number;
     /**
-     * Flag spots as ice rings and reduce their effect on indexing
+     * Flag spots as ice rings and reduce their effect on indexing. Left out, the broker's own
+     * spot finding treats no spot as an ice ring, rugnux live decides as a bare `rugnux` would (on
+     * for a rotation sweep, off for stills), and the master file carries no `detect_ice_rings`.
+     *
      */
     detect_ice_rings?: boolean;
     /**
diff --git a/receiver/JFJochReceiverRugnuxRotation.cpp b/receiver/JFJochReceiverRugnuxRotation.cpp
index b7d40a13a..aa33f0ca2 100644
--- a/receiver/JFJochReceiverRugnuxRotation.cpp
+++ b/receiver/JFJochReceiverRugnuxRotation.cpp
@@ -267,7 +267,7 @@ void JFJochReceiverRugnuxRotation::RugnuxThread() {
         std::optional<Reachable> reachable;
         reachable.emplace(rugnux_mutex, rugnux, *process, cut, cancelled);
         ProcessResult result = process->Run(&observer);
-        // The verdict and summary of the report a `rugnux` run writes, without writing it.
+        // The report a `rugnux` run writes, for the writer to write: its verdict and summary for the status as well.
         const ReportDocument doc = BuildReportDocument(experiment.GetFilePrefix(), experiment.GetFilePrefix(),
                                                        setup.experiment, result);
         // A cancelled collection is no failed analysis, and the run stops at the images that came
@@ -310,8 +310,9 @@ void JFJochReceiverRugnuxRotation::RugnuxThread() {
         live_status.Headline(result.space_group ? result.space_group->xhm() : "", d_min, isa);
         if (result.has_merge_statistics) {
             const ModelValidationResult *validation = result.model_validation ? &*result.model_validation : nullptr;
+            const RefinementResult *refinement = result.refinement ? &*result.refinement : nullptr;
             live_status.Shells("the collection", LiveShells(result.merge_statistics, validation),
-                               LiveOverall(result.merge_statistics, validation));
+                               LiveOverall(result.merge_statistics, validation, refinement));
             live_status.Frames(result.end_message.image_scale_factor, LiveFrameRanges(result.merge_statistics.sweep_quality));
         }
         // For the broker's viewer routes; a copy of the map coefficients, as the end message takes the originals
@@ -322,9 +323,11 @@ void JFJochReceiverRugnuxRotation::RugnuxThread() {
         }
         live_status.Finish(result.cancelled ? RugnuxLiveState::Cancelled : RugnuxLiveState::Done);
         reachable.reset();
+        std::string report = RenderReportText(doc, false);
         {
             std::unique_lock ul(rugnux_mutex);
             rugnux_result = std::move(result);
+            rugnux_report = std::move(report);
         }
         published = true;
         rugnux_published.set_value();
@@ -407,6 +410,7 @@ void JFJochReceiverRugnuxRotation::AddToEndMessage(EndMessage &message) {
         message.refined_poni_rot2 = rugnux_end.refined_poni_rot2;
         message.refined_poni_rot3 = rugnux_end.refined_poni_rot3;
         message.refined_rotation_axis = rugnux_end.refined_rotation_axis;
+        message.report = rugnux_report;
         // For the writer to write beside the master; moved, the result is not read again
         if (!rugnux_result->outputs)
             return;
diff --git a/receiver/JFJochReceiverRugnuxRotation.h b/receiver/JFJochReceiverRugnuxRotation.h
index 2fbf4fc60..beb0b46df 100644
--- a/receiver/JFJochReceiverRugnuxRotation.h
+++ b/receiver/JFJochReceiverRugnuxRotation.h
@@ -29,6 +29,7 @@ class JFJochReceiverRugnuxRotation : public JFJochReceiverStream {
     Rugnux *rugnux = nullptr;   // while it runs, for Cut
     Rugnux *probe = nullptr;    // the same for the lattice probe
     std::optional<ProcessResult> rugnux_result;
+    std::string rugnux_report;   // its _report.txt, for the writer
     std::promise<void> rugnux_published;   // rugnux_result is in place, or the run has failed (RugnuxThread)
     bool cut = false;
 
diff --git a/receiver/RugnuxLiveStatus.cpp b/receiver/RugnuxLiveStatus.cpp
index 7304a1149..b32a2d2ca 100644
--- a/receiver/RugnuxLiveStatus.cpp
+++ b/receiver/RugnuxLiveStatus.cpp
@@ -17,16 +17,27 @@ namespace {
             out = v;
     }
 
+    // The refined model's R-work and R-free: after the restrained stage, else after the rigid body and grouped B
+    double RefinedRWork(const RefinementResult &rf) {
+        return rf.restrained ? rf.r_work : rf.r_work_placement;
+    }
+
+    double RefinedRFree(const RefinementResult &rf) {
+        return rf.restrained ? rf.r_free : rf.r_free_placement;
+    }
+
     // The validation's shells are the merge's, labelled by the same d_min (report_shell_d_min); its overall R-free
-    // is the overall row's
+    // is the overall row's - unless the model was refined, when the overall row is the refined model's
     void AddShellRFree(std::vector<RugnuxLiveShell> &shells, std::optional<RugnuxLiveShell> &overall,
-                       const ModelValidationResult &validation) {
+                       const ModelValidationResult &validation, const RefinementResult *refinement) {
         for (const auto &m : validation.cc_model_shells)
             for (auto &sh : shells)
                 if (static_cast<float>(sh.d_min) == m.d_min && m.n_free > 0)
                     SetIfFinite(sh.r_free, m.r_free);
         if (overall && validation.ok)
             SetIfFinite(overall->r_free, validation.r_free);
+        if (overall && refinement && refinement->ok)
+            SetIfFinite(overall->r_free, RefinedRFree(*refinement));
     }
 
     // A row of the report's shell table - a shell, or the overall row
@@ -193,10 +204,11 @@ void RugnuxLiveStatus::Shells(const std::string &merge, const std::vector<Rugnux
     snapshot.overall = overall;
 }
 
-void RugnuxLiveStatus::ShellRFree(const std::string &merge, const ModelValidationResult &validation) {
+void RugnuxLiveStatus::ShellRFree(const std::string &merge, const ModelValidationResult &validation,
+                                  const RefinementResult *refinement) {
     std::unique_lock ul(status_mutex);
     if (snapshot.shells_merge == merge)
-        AddShellRFree(snapshot.shells, snapshot.overall, validation);
+        AddShellRFree(snapshot.shells, snapshot.overall, validation, refinement);
 }
 
 void RugnuxLiveStatus::Frames(const std::vector<float> &scales, const std::vector<RugnuxLiveFrameRange> &ranges) {
@@ -287,15 +299,16 @@ std::vector<RugnuxLiveShell> LiveShells(const MergeStatistics &statistics, const
             ret.push_back(LiveShell(in, statistics.stills));
     std::optional<RugnuxLiveShell> no_overall;
     if (validation)
-        AddShellRFree(ret, no_overall, *validation);
+        AddShellRFree(ret, no_overall, *validation, nullptr);
     return ret;
 }
 
-RugnuxLiveShell LiveOverall(const MergeStatistics &statistics, const ModelValidationResult *validation) {
+RugnuxLiveShell LiveOverall(const MergeStatistics &statistics, const ModelValidationResult *validation,
+                            const RefinementResult *refinement) {
     std::vector<RugnuxLiveShell> no_shells;
     std::optional<RugnuxLiveShell> ret = LiveShell(statistics.overall, statistics.stills);
     if (validation)
-        AddShellRFree(no_shells, ret, *validation);
+        AddShellRFree(no_shells, ret, *validation, refinement);
     return *ret;
 }
 
@@ -355,8 +368,8 @@ std::optional<RugnuxLiveModel> LiveModel(const ProcessResult &result) {
         r.on_gpu = rf.on_gpu;
         r.seconds = rf.seconds;
         if (rf.ok) {
-            SetIfFinite(r.r_work, rf.restrained ? rf.r_work : rf.r_work_placement);
-            SetIfFinite(r.r_free, rf.restrained ? rf.r_free : rf.r_free_placement);
+            SetIfFinite(r.r_work, RefinedRWork(rf));
+            SetIfFinite(r.r_free, RefinedRFree(rf));
             if (rf.restrained) {
                 SetIfFinite(r.rmsd_bonds_A, rf.geometry.rmsd_bonds);
                 SetIfFinite(r.rmsd_angles_deg, rf.geometry.rmsd_angles);
diff --git a/receiver/RugnuxLiveStatus.h b/receiver/RugnuxLiveStatus.h
index 902de6e90..e770e93cf 100644
--- a/receiver/RugnuxLiveStatus.h
+++ b/receiver/RugnuxLiveStatus.h
@@ -17,6 +17,7 @@ struct ReportDocument;    // rugnux/ReportDocument.h
 struct MergeStatistics;   // image_analysis/scale_merge/Merge.h
 struct SweepQuality;      // image_analysis/scale_merge/Merge.h
 struct ModelValidationResult;   // image_analysis/structure_refinement/ModelValidation.h
+struct RefinementResult;        // image_analysis/structure_refinement/Refinement.h
 
 // Where the live rugnux run of the last collection is.
 // Times come from the image puller (when a message came off the socket) and are in seconds since the first image arrived.
@@ -104,7 +105,9 @@ struct RugnuxLiveShell {
     std::optional<double> cc_half;
     std::optional<double> cc_ref;          // against a reference
     std::optional<double> r_split;         // stills only
-    std::optional<double> r_free;          // of the placed model, where a model was given
+    // Of the placed model, where a model was given. The overall row: of the model the run ended with - refined
+    // where the refinement ran (RugnuxLiveRefinement's), else as placed.
+    std::optional<double> r_free;
 };
 
 // A stretch of a rotation sweep the merge downgraded or rejected (SweepQuality), with what was seen there
@@ -214,8 +217,10 @@ public:
     void Stills(const RugnuxLiveStills &stills);
     void Shells(const std::string &merge, const std::vector<RugnuxLiveShell> &shells,
                 const std::optional<RugnuxLiveShell> &overall);
-    // The R-free by shell of a model placed on a merge, if that merge's table is the one shown
-    void ShellRFree(const std::string &merge, const ModelValidationResult &validation);
+    // The R-free by shell of a model placed on a merge, if that merge's table is the one shown; overall that of the
+    // refined model where it was refined
+    void ShellRFree(const std::string &merge, const ModelValidationResult &validation,
+                    const RefinementResult *refinement = nullptr);
     void Frames(const std::vector<float> &scales, const std::vector<RugnuxLiveFrameRange> &ranges);
     // Back to Idle with nothing of the last run, as before any collection.
     void Clear();
@@ -232,8 +237,10 @@ std::optional<RugnuxLiveModel> LiveModel(const ProcessResult &result);
 std::vector<RugnuxLiveShell> LiveShells(const MergeStatistics &statistics,
                                         const ModelValidationResult *validation = nullptr);
 
-// The overall row of the same table, with the overall R-free of the model validated on it
-RugnuxLiveShell LiveOverall(const MergeStatistics &statistics, const ModelValidationResult *validation = nullptr);
+// The overall row of the same table, with the overall R-free of the model validated on it - or of the model refined,
+// where it was
+RugnuxLiveShell LiveOverall(const MergeStatistics &statistics, const ModelValidationResult *validation = nullptr,
+                            const RefinementResult *refinement = nullptr);
 
 // The stretches of the sweep that were not merged at face value: the runs of one disposition in the
 // per-image array of the sweep-quality diagnostic, each with the reason of the range it lies in
diff --git a/receiver/StillsGPUAnalysis.cpp b/receiver/StillsGPUAnalysis.cpp
index 98e95b32e..9dfa19eab 100644
--- a/receiver/StillsGPUAnalysis.cpp
+++ b/receiver/StillsGPUAnalysis.cpp
@@ -581,7 +581,7 @@ void StillsGPUAnalysis::PublishModel(const ModelStepResult &result, const std::s
     if (const auto live_model = LiveModel(ModelStepReport(result)))
         status.Model(*live_model);
     if (result.validation)
-        status.ShellRFree(title, *result.validation);
+        status.ShellRFree(title, *result.validation, result.refinement ? &*result.refinement : nullptr);
     if (!result.placed_model)
         return;
     std::optional<PlacedModelOutput> refined;
diff --git a/tests/JFJochReceiverRugnuxTest.cpp b/tests/JFJochReceiverRugnuxTest.cpp
index fe2ccb643..16ecb3bd2 100644
--- a/tests/JFJochReceiverRugnuxTest.cpp
+++ b/tests/JFJochReceiverRugnuxTest.cpp
@@ -711,6 +711,12 @@ TEST_CASE("JFJochReceiverRugnux_Rotation", "[JFJochReceiverRugnux]") {
     CHECK(live.state != RugnuxLiveState::Running);
     // The report's checklist comes with its verdict
     CHECK(live.verdict.empty() == live.triage.empty());
+    // And the report itself goes to the writer, for <file_prefix>_report.txt
+    const auto end = pusher.End();
+    REQUIRE(end);
+    CHECK(end->report.has_value() == !live.verdict.empty());
+    if (end->report)
+        CHECK(end->report->find("\nVERDICT= " + live.verdict + "\n") != std::string::npos);
 }
 
 TEST_CASE("JFJochReceiverRugnux_Rotation_DoesNotFit", "[JFJochReceiverRugnux]") {
diff --git a/tests/RugnuxLiveStatusTest.cpp b/tests/RugnuxLiveStatusTest.cpp
index 57a6a1471..09dbc44d9 100644
--- a/tests/RugnuxLiveStatusTest.cpp
+++ b/tests/RugnuxLiveStatusTest.cpp
@@ -545,3 +545,51 @@ TEST_CASE("RugnuxLiveShells_AreTheReportTable", "[RugnuxLive]") {
         CHECK(!j.contains("overall"));
     }
 }
+
+TEST_CASE("RugnuxLiveStatus_OverallRFreeIsTheFinalModels", "[RugnuxLive]") {
+    MergeStatistics ms;
+    ms.shells = {TestShell(50.0, 4.0, 4000, 1000, 1010), TestShell(4.0, 2.2, 3000, 1000, 1050)};
+    ms.overall = TestShell(50.0, 2.2, 7000, 2000, 2060);
+    ModelValidationResult v;
+    v.ok = true;
+    v.r_work = 0.40;
+    v.r_free = 0.42;
+    v.cc_model_shells = {{4.0f, 0.9, 900, NAN, NAN, NAN, 0.35, 50}, {2.2f, 0.8, 900, NAN, NAN, NAN, 0.47, 45}};
+    RefinementResult rf;
+    rf.ok = true;
+    rf.r_work_placement = 0.36;
+    rf.r_free_placement = 0.39;
+    rf.restrained = true;
+    rf.r_work = 0.33;
+    rf.r_free = 0.37;
+
+    // Not refined: the placed model's, as the report's R_FREE
+    CHECK(LiveOverall(ms, &v).r_free.value() == Catch::Approx(0.42));
+    RefinementResult failed;
+    CHECK(LiveOverall(ms, &v, &failed).r_free.value() == Catch::Approx(0.42));
+    // Refined: the refined model's, as model.refinement.r_free and the report's REFINE_R_FREE
+    CHECK(LiveOverall(ms, &v, &rf).r_free.value() == Catch::Approx(0.37));
+    rf.restrained = false;
+    CHECK(LiveOverall(ms, &v, &rf).r_free.value() == Catch::Approx(0.39));
+    rf.restrained = true;
+
+    ProcessResult r;
+    r.model_validation = v;
+    r.model_placement = "RIGID_BODY";
+    r.refinement = rf;
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    status.Model(*LiveModel(r));
+    status.Shells("the collection", LiveShells(ms, &v), LiveOverall(ms, &v, &rf));
+    nlohmann::json j = Convert(status.Get());
+    CHECK(j["overall"]["r_free"].get<double>() == j["model"]["refinement"]["r_free"].get<double>());
+    CHECK(j["model"]["r_free"].get<double>() == Catch::Approx(0.42));
+    // The shells stay the placed model's: the refinement measures no shell
+    CHECK(j["shells"][0]["r_free"].get<double>() == Catch::Approx(0.35));
+
+    // Serial: the model placed on a merge and refined after its table was shown
+    status.Shells("the collection", LiveShells(ms), LiveOverall(ms));
+    status.ShellRFree("the collection", v, &rf);
+    CHECK(status.Get().overall->r_free.value() == Catch::Approx(0.37));
+    CHECK(status.Get().shells[1].r_free.value() == Catch::Approx(0.47));
+}
diff --git a/tests/RugnuxResultFilesTest.cpp b/tests/RugnuxResultFilesTest.cpp
index b61576637..5c877bf4e 100644
--- a/tests/RugnuxResultFilesTest.cpp
+++ b/tests/RugnuxResultFilesTest.cpp
@@ -24,6 +24,8 @@
 #include "../writer/WriteModel.h"
 #include "../writer/WriteRugnuxFiles.h"
 #include "../writer/RugnuxResultBlocks.h"
+#include "../rugnux/ResultReport.h"
+#include "../rugnux/RugnuxOutputFiles.h"
 #include "SyntheticMergedReflections.h"
 
 namespace {
@@ -415,3 +417,52 @@ TEST_CASE("RugnuxResultFiles: the refinement's model, maps and blobs reach the w
 
     std::filesystem::remove_all(dir);
 }
+
+TEST_CASE("RugnuxResultFiles: the results report reaches the writer through the END block as rugnux writes it",
+          "[rugnux_result_files]") {
+    Logger logger("RugnuxResultFiles");
+    const std::filesystem::path dir = std::filesystem::temp_directory_path() / "rugnux_result_files_report";
+    std::filesystem::remove_all(dir);
+    std::filesystem::create_directories(dir);
+    const std::string original = (dir / "rugnux").string();
+    const std::string written = (dir / "writer").string();
+
+    DiffractionExperiment x(DetJF(1));
+    x.ImagesPerTrigger(600);
+    ProcessResult result;
+    result.images_processed = 600;
+    result.consensus_cell = TEST_CELL;
+    result.space_group = *gemmi::find_spacegroup_by_name("P 43 21 2");
+
+    // As rugnux writes it (WriteResultReport), and as the broker puts it in the END message
+    // (JFJochReceiverRugnuxRotation): the text of the same document
+    const ReportDocument doc = WriteResultReport(original, "in.h5", x, result, logger);
+    EndMessage end{};
+    end.report = RenderReportText(doc, false);
+    std::vector<uint8_t> buffer(16 * 1024 * 1024);
+    CBORStream2Serializer serializer(buffer.data(), buffer.size());
+    REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(end));
+    auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
+    REQUIRE(deserialized);
+    REQUIRE(deserialized->end_message);
+    REQUIRE(deserialized->end_message->report);
+    WriteRugnuxResultFiles(*deserialized->end_message, written, false, logger);
+    CHECK(ReadFile(written + "_report.txt") == ReadFile(original + "_report.txt"));
+    CHECK(!std::filesystem::exists(written + "_report.txt.tmp"));
+    CHECK(!std::filesystem::exists(written + ".mtz"));
+
+    // A report is tens of kB, longer than a string of the stream used to be read back
+    end.report = std::string(100000, 'r') + "\n";
+    CBORStream2Serializer long_serializer(buffer.data(), buffer.size());
+    REQUIRE_NOTHROW(long_serializer.SerializeSequenceEnd(end));
+    deserialized = CBORStream2Deserialize(buffer.data(), long_serializer.GetBufferSize());
+    REQUIRE(deserialized->end_message->report);
+    CHECK(*deserialized->end_message->report == *end.report);
+
+    // No report, no file
+    EndMessage none{};
+    WriteRugnuxResultFiles(none, written + "_none", false, logger);
+    CHECK(!std::filesystem::exists(written + "_none_report.txt"));
+
+    std::filesystem::remove_all(dir);
+}
diff --git a/writer/WriteRugnuxFiles.cpp b/writer/WriteRugnuxFiles.cpp
index b8da75e2f..ddeb0f062 100644
--- a/writer/WriteRugnuxFiles.cpp
+++ b/writer/WriteRugnuxFiles.cpp
@@ -184,6 +184,16 @@ void RenameIntoPlace(const std::string &tmp, const std::string &final_name, bool
     logger.Info("{} written, renamed into place at wall clock {:.3f} s", final_name, WallClockSeconds());
 }
 
+// `text` as the file `filename`, written under a temporary name and renamed into place.
+void WriteTextFile(const std::string &text, const std::string &filename, bool overwrite, Logger &logger) {
+    {
+        std::ofstream f(filename + ".tmp", std::ofstream::out | std::ofstream::trunc);
+        f.exceptions(std::ios::failbit | std::ios::badbit);
+        f << text;
+    }
+    RenameIntoPlace(filename + ".tmp", filename, overwrite, logger);
+}
+
 // A file jfjoch_writer writes came out of two programs, and says so: Rugnux processed the data inside the
 // Jungfraujoch broker, which collected them. The reflection tables name Rugnux in their first HISTORY
 // record and the map tables carry none, so Rugnux is put first where nothing is; Jungfraujoch goes right
@@ -260,16 +270,15 @@ void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefi
         logger.Error("Cannot write {}_refined_maps.mtz: {}", file_prefix, e.what());
     }
     try {
-        if (end.blobs) {
-            const std::string text = DensityBlobsJson(*end.blobs);
-            {
-                std::ofstream f(file_prefix + "_blobs.json.tmp", std::ofstream::out | std::ofstream::trunc);
-                f.exceptions(std::ios::failbit | std::ios::badbit);
-                f << text;
-            }
-            RenameIntoPlace(file_prefix + "_blobs.json.tmp", file_prefix + "_blobs.json", overwrite, logger);
-        }
+        if (end.blobs)
+            WriteTextFile(DensityBlobsJson(*end.blobs), file_prefix + "_blobs.json", overwrite, logger);
     } catch (const std::exception &e) {
         logger.Error("Cannot write {}_blobs.json: {}", file_prefix, e.what());
     }
+    try {
+        if (end.report)
+            WriteTextFile(*end.report, file_prefix + "_report.txt", overwrite, logger);
+    } catch (const std::exception &e) {
+        logger.Error("Cannot write {}_report.txt: {}", file_prefix, e.what());
+    }
 }
diff --git a/writer/WriteRugnuxFiles.h b/writer/WriteRugnuxFiles.h
index 7345d7fe5..8103b53c2 100644
--- a/writer/WriteRugnuxFiles.h
+++ b/writer/WriteRugnuxFiles.h
@@ -30,8 +30,8 @@ std::string DensityBlobsJson(const DensityBlobsMessage &blobs);
 
 // The files above, from whichever blocks `end` carries, at <file_prefix>.mtz, _maps.mtz and _model.cif
 // (WritePlacedModel adds _model.pdb where a PDB can hold the cell), and the refinement's
-// _refined_model.cif (.pdb), _refined_maps.mtz and _blobs.json. Each is written under a temporary name and
-// renamed into place. An existing file is replaced only with `overwrite`; otherwise it is kept and the
+// _refined_model.cif (.pdb), _refined_maps.mtz and _blobs.json, and the results report _report.txt. Each is
+// written under a temporary name and renamed into place. An existing file is replaced only with `overwrite`; otherwise it is kept and the
 // new one is not written. Each names Jungfraujoch beside Rugnux as the software that made it: the MTZ
 // files in a HISTORY record, the models in their _software loop.
 void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefix, bool overwrite,