1.0.0-rc.174 (#84)

* Rugnux: Performance improvements on GPU and CPU (more of the pre-scan and of scaling on the GPU, faster CPU spot finding and crystal refinement), with unchanged results.
* Rugnux: More robust processing - patches of persistently hot pixels are masked, an inconsistent merge triggers a retry at the measured beam centre, and builds targeting different CPU levels give the same results.
* Rugnux: Improved scaling and merging - reflections with an overloaded pixel are dropped, as in XDS, sparse rotation sweeps are scaled more reliably, and French-Wilson amplitudes use an anisotropic Wilson prior.
* Rugnux: Improved space-group determination - glide planes in groups without a centre of symmetry, screw axes from short or weak axial rows kept when a higher group is adopted, and more reliable decisions on twinned and pseudo-symmetric crystals.
* Rugnux: Improved small-molecule processing - spots that grow wider than the integration disk and split spots are integrated over their measured footprint, sparse lattices are integrated on every frame, and the `.hkl` file holds unmerged scaled reflections (SHELX HKLF 4).
* Rugnux: Reads Rigaku d*TREK SMV images (Saturn CCD), including detector 2theta and encoded pixel overflows; home-source (rotating-anode) datasets were added to the validation battery.
* jfjoch_viewer: Fixed processing failing at the end with "Wrong JPEG library version" on Linux; the merge window shows the space group with proper subscripts and a checklist of crystal pathologies.

Reviewed-on: #84
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

docs/python_client/README.md

@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.173
-- Package version: 1.0.0-rc.173
+- API version: 1.0.0-rc.174
+- Package version: 1.0.0-rc.174
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 
@@ -237,7 +237,12 @@ Class | Method | HTTP request | Description
 <a id="documentation-for-authorization"></a>
 ## Documentation For Authorization
 
-Endpoints do not require authorization.
+
+Authentication schemes defined for the API:
+<a id="bearerAuth"></a>
+### bearerAuth
+
+- **Type**: Bearer authentication
 
 
 ## Author

docs/python_client/docs/DatasetSettings.md

@@ -45,6 +45,7 @@ Name | Type | Description | Notes
 **max_spot_count** | **int** | Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected | [optional] [default to 250]
 **detect_ice_rings** | **bool** | Flag spots as ice rings and reduce their effect on indexing | [optional] 
 **async_start** | **bool** | When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement. | [optional] [default to False]
+**tokens** | **List[str]** | Bearer tokens that protect this dataset: any number, all equivalent (e.g. a beamline secret and a dataset-specific user secret). While set, the endpoints marked with the `bearerAuth` security scheme require `Authorization: Bearer <token>` and answer 401 otherwise. Every accepted `/start` replaces the previous dataset's tokens; omitted or empty means no protection. Never returned by any endpoint.  | [optional] 
 **xray_fluorescence_spectrum** | [**DatasetSettingsXrayFluorescenceSpectrum**](DatasetSettingsXrayFluorescenceSpectrum.md) |  | [optional] 
 
 ## Example

docs/python_client/docs/DefaultApi.md

@@ -2801,6 +2801,7 @@ Contains full image data and metadata. The image must come from the latest data
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -2813,6 +2814,15 @@ 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:
@@ -2844,17 +2854,18 @@ Name | Type | Description  | Notes
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/cbor, application/json
+ - **Accept**: text/plain, application/cbor, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Return image message |  -  |
 **404** | Image not present in the buffer - either not yet measured or already replaced by a next image. |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
@@ -2868,6 +2879,7 @@ Get preview image in JPEG format using custom settings
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -2880,6 +2892,15 @@ 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:
@@ -2931,17 +2952,18 @@ Name | Type | Description  | Notes
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: image/jpeg, text/plain, application/json
+ - **Accept**: text/plain, image/jpeg, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Preview image |  -  |
 **404** | Image not present in the buffer - either not yet measured or already replaced by a next image. |  -  |
 **400** | Input parsing or validation error |  -  |
@@ -2956,6 +2978,7 @@ Get preview image in TIFF format
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -2968,6 +2991,15 @@ 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:
@@ -2999,17 +3031,18 @@ Name | Type | Description  | Notes
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: image/tiff
+ - **Accept**: text/plain, image/tiff
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Preview image |  -  |
 **404** | No preview image recorded so far |  -  |
 
@@ -3024,6 +3057,7 @@ Contains metadata for a dataset (e.g., experimental geometry)
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -3036,6 +3070,15 @@ 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:
@@ -3063,17 +3106,18 @@ This endpoint does not need any parameter.
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/cbor, application/json
+ - **Accept**: text/plain, application/cbor, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Return start message |  -  |
 **404** | No measurement so far |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
@@ -3425,6 +3469,7 @@ Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provi
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -3437,6 +3482,15 @@ 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:
@@ -3470,17 +3524,18 @@ Name | Type | Description  | Notes
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/octet-stream, text/plain
+ - **Accept**: text/plain, application/octet-stream
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK. |  -  |
 **400** | Input parsing or validation error |  -  |
 
@@ -3493,6 +3548,7 @@ Generate 1D plot from Jungfraujoch
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -3506,6 +3562,15 @@ 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:
@@ -3545,17 +3610,18 @@ Name | Type | Description  | Notes
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/json, text/plain
+ - **Accept**: text/plain, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK. |  -  |
 **400** | Input parsing or validation error |  -  |
 
@@ -3568,6 +3634,7 @@ Get full scan result
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -3581,6 +3648,15 @@ 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:
@@ -3608,17 +3684,18 @@ This endpoint does not need any parameter.
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/json
+ - **Accept**: text/plain, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK. |  -  |
 **404** | No grid scan recorded |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
@@ -3635,6 +3712,8 @@ Detector must be in `Idle` state.
 Default behavior is for the call to block until detector is ready to accept soft/TTL triggers.
 However, this behavior can be changed by settings `async_start` to true in the request body, 
 in which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.
+Optional `tokens` protect the dataset: while set, its statistics, buffered images and plots
+require `Authorization: Bearer <token>`.
 
 
 ### Example
@@ -3767,10 +3846,11 @@ No authorization required
 
 Get data collection statistics
 
-Results of the last data collection
+Results of the last data collection (dataset name, unit cell, ...)
 
 ### Example
 
+* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -3784,6 +3864,15 @@ 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:
@@ -3811,17 +3900,18 @@ This endpoint does not need any parameter.
 
 ### Authorization
 
-No authorization required
+[bearerAuth](../README.md#bearerAuth)
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/json
+ - **Accept**: text/plain, application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK |  -  |
 **404** | No data collection performed so far |  -  |
 
@@ -3832,6 +3922,10 @@ No authorization required
 
 Get general statistics
 
+`measurement` is omitted unless the request carries a valid bearer token for a protected
+dataset (see `tokens` in `/start`).
+
+
 ### Example