rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG

The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, as one change on main. The individual commits stay on the rc178 branch:

- still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes
- AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets
- DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
- tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout
- Dense per-pixel maps through the panel table (panel layout stage 1)
- Panel id on spots and the panel table in the start message
- Viewer and preview show a panel detector as it lies on the detector plane
- Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
- Panel layout stage 2: prediction and Bragg integration through the panel table
- XTC reader: frames handed up as stored, streams indexed in parallel
- XFEL reader: integer frames stay integer, one gain, placement by panel
- EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery"
- still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed
- float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count
- CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
- Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
- Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane
- still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good
- still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file
- still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition
- stills fixed cost: geometry refinement and pre-scan do the same work in less wall time
- stills geometry sample and trial spot finding run as many workers as the image pass
- Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame
- StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's
- MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in)
- Stills given a cell: the written cell is the mean over the frames that are merged
- Stills: the radial curvature correction decided per run on the same empty apertures
- StillsPartialityRefine: measure the run width only on shells with signal
- Stills pre-scan: report the paired z of the radial-correction comparison
- module placement: the five concurrent fits each keep every thread
- still battery: score R-free against the deposited data through the same dimple protocol
- still battery: the R-free target is the lower of the deposition's dimple and published values
- Stills: background clip follows the radial curve; signal disk from the lattice spacing
- Stills keep an overloaded observation as a lower bound instead of dropping it
- Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip
- battery: R-free against the deposition without refinement only, one protocol for rotation and stills
- still battery: EuXFEL sets run on a 2,000-image subset for now
- stills geometry refinement: fit the detector distance and the cell together
- stills geometry refinement: a distance given with --detector-distance is held in the joint fit
- Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count
- Metal integration test: the CPU comparison runs on a rotation experiment
- Stills: kept overloads go back to the drop where they are not concentrated at low resolution
- stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated
- battery results: XFEL still battery 20261022-1358 on rc178 0cf62452c - 12 sets, cold, R_free unrefined
- battery results: still summary gains the resolution of our merge and of the deposition
- Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value
- Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
- XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock
- stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes
- rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid
- stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree
- CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get
- broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
- frontend: Mol* viewer of the placed model and its density on the Rugnux live page
- writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
- rugnux live maps: one unit cell centred on the model; the viewer opens on all of it
- Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer
- Mol* viewer: open with the maps drawn within 10 A of the centre of view
- Mol* viewer: aaredb's structure-viewer setup, on a black stage
- rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons
- Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2)
- ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI)
- stills tilt decision: the modules stay where the run placed them
- still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it
- battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC
- Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons
- BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it
- ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization
- BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain
- ShadowFinder: measure the modulation robustly under a wide one-sided shadow
- ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation
- ShadowFinder: back to the predicted polarization factor, in the plane the background shows
- MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again
- battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables
- XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
- stills geometry trial: the hypotheses a search asks are indexed side by side
- stills tilt decision: the fits start beside the pre-scan and the geometry trial
- XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache
- XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step
- GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block
- GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart
- docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts
- battery: doc_check.py cross-checks the manifests against the dataset pages
- stills module placement: the placement fit gets half the threads, each held-out fit an eighth
- still battery: the EuXFEL sets run on all their frames, as the published still runs did
- battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table
- macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu

docs/python_client/README.md

@@ -159,6 +159,8 @@ Class | Method | HTTP request | Description
 *DefaultApi* | [**preview_plot_bin_get**](docs/DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. 
 *DefaultApi* | [**preview_plot_get**](docs/DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
 *DefaultApi* | [**result_scan_get**](docs/DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
+*DefaultApi* | [**rugnux_map_ccp4_get**](docs/DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
+*DefaultApi* | [**rugnux_model_cif_get**](docs/DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
 *DefaultApi* | [**rugnux_status_get**](docs/DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
 *DefaultApi* | [**start_post**](docs/DefaultApi.md#start_post) | **POST** /start | Start detector
 *DefaultApi* | [**statistics_calibration_get**](docs/DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics

docs/python_client/docs/DefaultApi.md

@@ -62,6 +62,8 @@ Method | HTTP request | Description
 [**preview_plot_bin_get**](DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. 
 [**preview_plot_get**](DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
 [**result_scan_get**](DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
+[**rugnux_map_ccp4_get**](DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
+[**rugnux_model_cif_get**](DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
 [**rugnux_status_get**](DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
 [**start_post**](DefaultApi.md#start_post) | **POST** /start | Start detector
 [**statistics_calibration_get**](DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics
@@ -4073,6 +4075,168 @@ This endpoint does not need any parameter.
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
+# **rugnux_map_ccp4_get**
+> bytearray rugnux_map_ccp4_get(type=type)
+
+Get an electron-density map of the last rugnux live run
+
+The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
+coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
+the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
+RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+
+
+### Example
+
+* Bearer Authentication (bearerAuth):
+
+```python
+import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+# Configure Bearer authorization: bearerAuth
+configuration = jfjoch_client.Configuration(
+    access_token = os.environ["BEARER_TOKEN"]
+)
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    type = 2fofc # str | `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map` in `/rugnux/status`)  (optional) (default to 2fofc)
+
+    try:
+        # Get an electron-density map of the last rugnux live run
+        api_response = api_instance.rugnux_map_ccp4_get(type=type)
+        print("The response of DefaultApi->rugnux_map_ccp4_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->rugnux_map_ccp4_get: %s\n" % e)
+```
+
+
+
+### Parameters
+
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **type** | **str**| `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map` in `/rugnux/status`)  | [optional] [default to 2fofc]
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+[bearerAuth](../README.md#bearerAuth)
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: application/octet-stream, text/plain
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Map |  -  |
+**400** | Unknown map type |  -  |
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
+**404** | The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
+# **rugnux_model_cif_get**
+> bytearray rugnux_model_cif_get()
+
+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 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
+
+* Bearer Authentication (bearerAuth):
+
+```python
+import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+# Configure Bearer authorization: bearerAuth
+configuration = jfjoch_client.Configuration(
+    access_token = os.environ["BEARER_TOKEN"]
+)
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get the model as placed by the last rugnux live run
+        api_response = api_instance.rugnux_model_cif_get()
+        print("The response of DefaultApi->rugnux_model_cif_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->rugnux_model_cif_get: %s\n" % e)
+```
+
+
+
+### Parameters
+
+This endpoint does not need any parameter.
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+[bearerAuth](../README.md#bearerAuth)
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: chemical/x-mmcif, text/plain
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Placed model |  -  |
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
+**404** | The last rugnux live run placed no model |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
 # **rugnux_status_get**
 > RugnuxLiveStatus rugnux_status_get()
 

docs/python_client/docs/RugnuxLiveStatus.md

@@ -7,6 +7,8 @@ Live rugnux processing of the last collection; kept until the next collection st
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **state** | **str** |  | 
+**placed_model** | **bool** | The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from `/rugnux/map.ccp4`.  | 
+**anomalous_map** | **bool** | The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map (`/rugnux/map.ccp4?type=anom`).  | 
 **probe** | **str** | Answer of the early lattice probe on the first 60 degrees; empty until it answers | 
 **probe_s** | **float** | When the probe answered, since the first image | [optional] 
 **start_to_first_image_s** | **float** | From the START message to the first image; set once the first image arrives | [optional]