diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index c64ba89b7..416219559 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -3615,9 +3615,9 @@ paths:
     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 coordinates, cell
-        and space group of the `_model.cif` file written beside the data, with the input model's own metadata
-        (entities, citation) kept. Kept as long as `/rugnux/status`.
+        The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+        `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
+        metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
       security:
         - bearerAuth: []
       responses:
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index da7f99e30..9e1fcf118 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -864,9 +864,9 @@ and validation of every following rugnux live collection, until it is removed wi
 </div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" 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></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" 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><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" 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><strong class="sc-dSIIpw bpEYcE">401<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The current dataset is protected and no valid bearer token was presented.</p>
 </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">/rugnux/status</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>/rugnux/status</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_jiia_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_jiia_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_jiia_0" aria-labelledby="tab_R_jiia_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"placed_model"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"start_to_first_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"expected_collection_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_received"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"elapsed_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"step_progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"steps"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"started_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"duration_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"notes"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_to_written_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict_text"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"summary"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"label"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"value"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"warnings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1rugnux~1model.cif/get" data-section-id="/paths/~1rugnux~1model.cif/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1rugnux~1model.cif/get" aria-label="/paths/~1rugnux~1model.cif/get"></a>Get the model as placed by the last rugnux live run<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
-and space group of the <code>_model.cif</code> file written beside the data, with the input model&#39;s own metadata
-(entities, citation) kept. Kept as long as <code>/rugnux/status</code>.</p>
+</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/rugnux/status</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_jiia_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_jiia_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_jiia_0" aria-labelledby="tab_R_jiia_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"placed_model"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"start_to_first_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"expected_collection_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_received"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"elapsed_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"step_progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"steps"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"started_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"duration_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"notes"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_to_written_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict_text"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"summary"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"label"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"value"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"warnings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1rugnux~1model.cif/get" data-section-id="/paths/~1rugnux~1model.cif/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1rugnux~1model.cif/get" aria-label="/paths/~1rugnux~1model.cif/get"></a>Get the model as placed by the last rugnux live run<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+<code>_model.cif</code> file written beside the data: the data&#39;s cell and space group, with the input model&#39;s own
+metadata (entities, sequences, references, authors, software) kept. Kept as long as <code>/rugnux/status</code>.</p>
 </div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" 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></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" 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><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Placed model</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" 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><strong class="sc-dSIIpw bpEYcE">401<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The current dataset is protected and no valid bearer token was presented.</p>
 </div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The last rugnux live run placed no model</p>
@@ -1113,7 +1113,7 @@ 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.178","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. 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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","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."},"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","quick_integration","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,"description":"Quick integration of Bragg spots in diffraction images.\nIf enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.\n(experimental feature)\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.\nOnly available 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,\nso enabling this there is rejected rather than silently ignored.\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","q_spacing"],"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]. 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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]. 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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 coordinates, cell\nand space group of the `_model.cif` file written beside the data, with the input model's own metadata\n(entities, citation) kept. Kept as long as `/rugnux/status`.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"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":"The last rugnux live run placed no model"}}}},"/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`. It covers the box around the model plus 5 A on every side, sampled\nevery d_min/3; the mean and RMS in its header are those of the whole unit cell, so contour levels in\nsigma are the usual ones.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type","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"}}}},"/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 - 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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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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. 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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","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."},"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","quick_integration","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,"description":"Quick integration of Bragg spots in diffraction images.\nIf enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.\n(experimental feature)\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.\nOnly available 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,\nso enabling this there is rejected rather than silently ignored.\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","q_spacing"],"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},"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"}}},"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]. 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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`.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"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":"The last rugnux live run placed no model"}}}},"/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`. It covers the box around the model plus 5 A on every side, sampled\nevery d_min/3; the mean and RMS in its header are those of the whole unit cell, so contour levels in\nsigma are the usual ones.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type","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"}}}},"/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 - 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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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
       var container = document.getElementById('redoc');
       Redoc.hydrate(__redoc_state, container);
diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index ec9ce70d6..e0da5f334 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -396,6 +396,13 @@ struct PlacedModelMessage {
     std::vector<double> x, y, z;
     std::vector<float> b_iso, occupancy;
     std::vector<float> aniso;              // 6 per atom (u11 u22 u33 u12 u13 u23), empty when none has one
+    // mmCIF label_asym_id, label_entity_id and label_seq_id per atom (label_seq INT32_MIN where none); empty
+    // in a block from before they were carried
+    std::vector<std::string> subchain, entity_id;
+    std::vector<int32_t> label_seq;
+    // The input model's metadata - entities, sequences, references, authors, software, secondary structure -
+    // as the mmCIF categories gemmi writes for them, without coordinates; empty where there is none
+    std::string metadata_mmcif;
 };
 
 struct EndMessage {
diff --git a/docs/CBOR.md b/docs/CBOR.md
index ddc46d4ab..d98a3c267 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -346,7 +346,7 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | image_scale_cc                   | Array(float)             | Scaling result: Image scale CC                                                                                                    |                           |
 | merged                           | object (optional)        | Merged reflections of an in-broker analysis run, written by the writer as `<file_prefix>.mtz`. An MTZ table (layout below) | |
 | map_coefficients                 | object (optional)        | Map coefficients of an in-broker analysis run, written as `<file_prefix>_maps.mtz`. An MTZ table (layout below) | |
-| placed_model                     | object (optional)        | Atomic model placed against the data, written as `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`. `name` (string), `unit_cell` (object, as above), `space_group_name` (the data's, gemmi extended H-M), `model_space_group_name` (the coordinates'), then one array per atom: `model_number`, `seq_num`, `charge` (int32), `chain`, `residue_name`, `atom_name`, `element` (Array(string)), `icode` (uint8, space where none), `het_flag` (uint8, `A`, `H` or 0 where unknown), `altloc` (uint8, 0 where none), `x`, `y`, `z` (double, Angstrom), `b_iso`, `occupancy` (float), `aniso` (float, 6 per atom: U11 U22 U33 U12 U13 U23; empty where no atom has one) | |
+| placed_model                     | object (optional)        | Atomic model placed against the data, written as `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`. `name` (string), `unit_cell` (object, as above), `space_group_name` (the data's, gemmi extended H-M), `model_space_group_name` (the coordinates'), then one array per atom: `model_number`, `seq_num`, `charge` (int32), `chain`, `residue_name`, `atom_name`, `element` (Array(string)), `icode` (uint8, space where none), `het_flag` (uint8, `A`, `H` or 0 where unknown), `altloc` (uint8, 0 where none), `x`, `y`, `z` (double, Angstrom), `b_iso`, `occupancy` (float), `aniso` (float, 6 per atom: U11 U22 U33 U12 U13 U23; empty where no atom has one), `subchain`, `entity_id` (Array(string), mmCIF label_asym_id / label_entity_id), `label_seq` (int32, label_seq_id, INT32_MIN where none) - these three optional; `metadata_mmcif` (string, optional): the input model's metadata (entities, sequences, references, authors, software, secondary structure) as mmCIF categories without coordinates, parsed by the writer with gemmi | |
 
 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/python_client/docs/DefaultApi.md b/docs/python_client/docs/DefaultApi.md
index f9d6dd334..22250ec15 100644
--- a/docs/python_client/docs/DefaultApi.md
+++ b/docs/python_client/docs/DefaultApi.md
@@ -4164,9 +4164,9 @@ Name | Type | Description  | Notes
 
 Get the model as placed by the last rugnux live run
 
-The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
-and space group of the `_model.cif` file written beside the data, with the input model's own metadata
-(entities, citation) kept. Kept as long as `/rugnux/status`.
+The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+`_model.cif` file written beside the data: the data's cell and space group, with the input model's own
+metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
 
 
 ### Example
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index a7c0dba3f..d6f4e647e 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -1669,6 +1669,10 @@ namespace {
             else if (key == "b_iso") GetCBORFloatArray(map_value, m.b_iso);
             else if (key == "occupancy") GetCBORFloatArray(map_value, m.occupancy);
             else if (key == "aniso") GetCBORFloatArray(map_value, m.aniso);
+            else if (key == "subchain") GetCBORStringArray(map_value, m.subchain);
+            else if (key == "entity_id") GetCBORStringArray(map_value, m.entity_id);
+            else if (key == "label_seq") GetCBORInt32Array(map_value, m.label_seq);
+            else if (key == "metadata_mmcif") m.metadata_mmcif = GetCBORString(map_value);
             else SkipCBORValue(map_value);
         }
         cborErr(cbor_value_leave_container(&value, &map_value));
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index 07412333e..4e9615615 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -623,6 +623,10 @@ inline void CBOR_ENC(CborEncoder &encoder, const char* key, const PlacedModelMes
     CBOR_ENC(mapEncoder, "b_iso", m.b_iso);
     CBOR_ENC(mapEncoder, "occupancy", m.occupancy);
     CBOR_ENC(mapEncoder, "aniso", m.aniso);
+    CBOR_ENC(mapEncoder, "subchain", m.subchain);
+    CBOR_ENC(mapEncoder, "entity_id", m.entity_id);
+    CBOR_ENC(mapEncoder, "label_seq", m.label_seq);
+    CBOR_ENC(mapEncoder, "metadata_mmcif", m.metadata_mmcif);
     cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
 }
 
diff --git a/frontend/src/client/@tanstack/react-query.gen.ts b/frontend/src/client/@tanstack/react-query.gen.ts
index 03d91ef6b..adc30d20b 100644
--- a/frontend/src/client/@tanstack/react-query.gen.ts
+++ b/frontend/src/client/@tanstack/react-query.gen.ts
@@ -790,9 +790,9 @@ export const getRugnuxModelCifQueryKey = (options?: Options<getRugnuxModelCifDat
 /**
  * Get the model as placed by the last rugnux live run
  *
- * The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
- * and space group of the `_model.cif` file written beside the data, with the input model's own metadata
- * (entities, citation) kept. Kept as long as `/rugnux/status`.
+ * The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+ * `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
+ * metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
  *
  */
 export const getRugnuxModelCifOptions = (options?: Options<getRugnuxModelCifData>) => queryOptions<getRugnuxModelCifResponse, getRugnuxModelCifError, getRugnuxModelCifResponse, ReturnType<typeof getRugnuxModelCifQueryKey>>({
diff --git a/frontend/src/client/sdk.gen.ts b/frontend/src/client/sdk.gen.ts
index 56c46a878..bbf928424 100644
--- a/frontend/src/client/sdk.gen.ts
+++ b/frontend/src/client/sdk.gen.ts
@@ -441,9 +441,9 @@ export const getRugnuxStatus = <ThrowOnError extends boolean = false>(options?:
 /**
  * Get the model as placed by the last rugnux live run
  *
- * The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
- * and space group of the `_model.cif` file written beside the data, with the input model's own metadata
- * (entities, citation) kept. Kept as long as `/rugnux/status`.
+ * The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+ * `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
+ * metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
  *
  */
 export const getRugnuxModelCif = <ThrowOnError extends boolean = false>(options?: Options<getRugnuxModelCifData, ThrowOnError>): RequestResult<getRugnuxModelCifResponses, getRugnuxModelCifErrors, ThrowOnError> => (options?.client ?? client).get<getRugnuxModelCifResponses, getRugnuxModelCifErrors, ThrowOnError>({
diff --git a/receiver/RugnuxStructure.h b/receiver/RugnuxStructure.h
index 188235a50..4142240ed 100644
--- a/receiver/RugnuxStructure.h
+++ b/receiver/RugnuxStructure.h
@@ -17,7 +17,7 @@
 enum class RugnuxMapType { TwoFoFc, FoFc };
 
 // The placed model and the map coefficients of a live rugnux run, for the broker to serve to a viewer: the
-// model as mmCIF, in the frame of <prefix>_model.cif (PlacedModelMmcif), and the maps as CCP4 map files - made in memory when
+// model as mmCIF, the same text as <prefix>_model.cif (PlacedModelMmcif), and the maps as CCP4 map files - made in memory when
 // first asked for and kept, never written to disk.
 class RugnuxStructure {
     std::shared_ptr<const gemmi::Structure> model;
diff --git a/tests/RugnuxResultFilesTest.cpp b/tests/RugnuxResultFilesTest.cpp
index 7f0b99792..8792a465d 100644
--- a/tests/RugnuxResultFilesTest.cpp
+++ b/tests/RugnuxResultFilesTest.cpp
@@ -270,3 +270,40 @@ TEST_CASE("RugnuxResultFiles: a placed model block that describes no model is re
     CHECK(!std::filesystem::exists(prefix + "_model.cif"));
     std::filesystem::remove_all(dir);
 }
+
+TEST_CASE("RugnuxResultFiles: the input model's metadata reaches _model.cif through the END block", "[rugnux_result_files]") {
+    Logger logger("RugnuxResultFiles");
+    const std::filesystem::path dir = std::filesystem::temp_directory_path() / "rugnux_result_files_metadata";
+    std::filesystem::remove_all(dir);
+    std::filesystem::create_directories(dir);
+    const std::string original = (dir / "rugnux").string();
+    const std::string written = (dir / "writer").string();
+
+    // A predicted model of a standard test protein (myoglobin), with entities, sequence references, authors and
+    // software, as a model given to rugnux carries them.
+    const gemmi::Structure st = gemmi::read_structure_gz("../../tools/battery/models/AF-P68082-F1-model_v6.cif");
+    const gemmi::SpaceGroup &p1 = *gemmi::find_spacegroup_by_name("P 1");
+    WritePlacedModel(st, TEST_CELL, p1, original, logger);
+
+    EndMessage end{};
+    end.placed_model = PlacedModelFromStructure(st, TEST_CELL, p1.xhm());
+    std::vector<uint8_t> buffer(MESSAGE_SIZE_FOR_START_END);
+    CBORStream2Serializer serializer(buffer.data(), buffer.size());
+    REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(end));
+    auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
+    REQUIRE(deserialized);
+    REQUIRE(deserialized->end_message);
+    WriteRugnuxResultFiles(*deserialized->end_message, written, false, logger);
+
+    const std::string cif = ReadFile(written + "_model.cif");
+    CHECK(cif == ReadFile(original + "_model.cif"));
+    CHECK(cif == PlacedModelMmcif(st, TEST_CELL, p1));   // what the broker serves at /rugnux/model.cif
+    for (const char *category : {"_audit_author.", "_entity_poly_seq.", "_struct_ref.", "_software.", "_struct_conf."})
+        CHECK(cif.find(category) != std::string::npos);
+    CHECK(ReadFile(written + "_model.pdb") == ReadFile(original + "_model.pdb"));
+    const gemmi::Structure back = gemmi::read_structure_gz(written + "_model.cif");
+    CHECK(gemmi::count_atom_sites(back) == gemmi::count_atom_sites(st));
+    CHECK(back.entities.size() == st.entities.size());
+
+    std::filesystem::remove_all(dir);
+}
diff --git a/writer/RugnuxResultBlocks.cpp b/writer/RugnuxResultBlocks.cpp
index de9ada77a..3da77af9f 100644
--- a/writer/RugnuxResultBlocks.cpp
+++ b/writer/RugnuxResultBlocks.cpp
@@ -3,6 +3,11 @@
 
 #include "RugnuxResultBlocks.h"
 
+#include <sstream>
+
+#include <gemmi/to_cif.hpp>     // write_cif_block_to_stream
+#include <gemmi/to_mmcif.hpp>   // make_mmcif_block
+
 PlacedModelMessage PlacedModelFromStructure(const gemmi::Structure &st, const UnitCell &cell,
                                             const std::string &data_space_group_name) {
     PlacedModelMessage p;
@@ -21,6 +26,9 @@ PlacedModelMessage PlacedModelFromStructure(const gemmi::Structure &st, const Un
                     p.seq_num.push_back(*r.seqid.num);
                     p.icode.push_back(static_cast<uint8_t>(r.seqid.icode));
                     p.het_flag.push_back(static_cast<uint8_t>(r.het_flag));
+                    p.subchain.push_back(r.subchain);
+                    p.entity_id.push_back(r.entity_id);
+                    p.label_seq.push_back(r.label_seq.value);
                     p.atom_name.push_back(a.name);
                     p.element.push_back(a.element.name());
                     p.altloc.push_back(static_cast<uint8_t>(a.altloc));
@@ -36,5 +44,14 @@ PlacedModelMessage PlacedModelFromStructure(const gemmi::Structure &st, const Un
                 }
     if (!has_aniso)
         p.aniso.clear();
+    // Everything of the model but its coordinates (and what goes with them: cell, symmetry, scale), as the mmCIF
+    // categories gemmi writes, for the writer to put back on _model.cif.
+    gemmi::MmcifOutputGroups groups(true);
+    groups.atoms = groups.cell = groups.symmetry = groups.scale = groups.atom_type = groups.origx = false;
+    // _entry.id would otherwise be made up from the name, which the block carries anyway.
+    groups.entry = st.info.count("_entry.id") > 0;
+    std::ostringstream os;
+    gemmi::cif::write_cif_block_to_stream(os, gemmi::make_mmcif_block(st, groups));
+    p.metadata_mmcif = os.str();
     return p;
 }
diff --git a/writer/WriteRugnuxFiles.cpp b/writer/WriteRugnuxFiles.cpp
index 32e57b4f9..a2e16b515 100644
--- a/writer/WriteRugnuxFiles.cpp
+++ b/writer/WriteRugnuxFiles.cpp
@@ -8,6 +8,8 @@
 #include <filesystem>
 
 #include <gemmi/mtz.hpp>
+#include <gemmi/read_cif.hpp>   // cif::read_string
+#include <gemmi/mmcif.hpp>   // make_structure_from_block
 
 #include "WriteModel.h"
 #include "../common/Logger.h"
@@ -70,6 +72,10 @@ gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model) {
         if (size != n)
             throw std::runtime_error(fmt::format("placed model: a per-atom field has {} entries for {} atoms",
                                                  size, n));
+    for (const size_t size : {model.subchain.size(), model.entity_id.size(), model.label_seq.size()})
+        if (size != 0 && size != n)
+            throw std::runtime_error(fmt::format("placed model: a per-atom label field has {} entries for {} atoms",
+                                                 size, n));
     if (!model.aniso.empty() && model.aniso.size() != 6 * n)
         throw std::runtime_error(fmt::format("placed model: {} anisotropic values for {} atoms",
                                              model.aniso.size(), n));
@@ -95,6 +101,12 @@ gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model) {
             || res->het_flag != static_cast<char>(model.het_flag[i])) {
             res = &ch->residues.emplace_back(gemmi::ResidueId{seqid, {}, model.residue_name[i]});
             res->het_flag = static_cast<char>(model.het_flag[i]);
+            if (!model.subchain.empty())
+                res->subchain = model.subchain[i];
+            if (!model.entity_id.empty())
+                res->entity_id = model.entity_id[i];
+            if (!model.label_seq.empty())
+                res->label_seq.value = model.label_seq[i];
         }
         gemmi::Atom &a = res->atoms.emplace_back();
         a.name = model.atom_name[i];
@@ -108,6 +120,24 @@ gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model) {
             a.aniso = {model.aniso[6 * i], model.aniso[6 * i + 1], model.aniso[6 * i + 2],
                        model.aniso[6 * i + 3], model.aniso[6 * i + 4], model.aniso[6 * i + 5]};
     }
+    if (!model.metadata_mmcif.empty()) {
+        // The input model's metadata, from the mmCIF categories it came as: parsed by gemmi, never copied.
+        gemmi::cif::Document doc = gemmi::cif::read_string(model.metadata_mmcif);
+        if (doc.blocks.empty())
+            throw std::runtime_error("placed model: the metadata block is empty");
+        gemmi::Structure meta = gemmi::make_structure_from_block(doc.blocks[0]);
+        st.entities = std::move(meta.entities);
+        st.connections = std::move(meta.connections);
+        st.cispeps = std::move(meta.cispeps);
+        st.mod_residues = std::move(meta.mod_residues);
+        st.helices = std::move(meta.helices);
+        st.sheets = std::move(meta.sheets);
+        st.assemblies = std::move(meta.assemblies);
+        st.ncs = std::move(meta.ncs);
+        st.meta = std::move(meta.meta);
+        st.info = std::move(meta.info);
+        st.resolution = meta.resolution;
+    }
     st.setup_cell_images();
     return st;
 }