jfjoch_broker: Add auto-contrast option

broker/JFJochBrokerHttp.cpp

@@ -478,6 +478,7 @@ void JFJochBrokerHttp::image_buffer_image_jpeg_get(const std::optional<int64_t>
                                                    const std::optional<int64_t> &jpegQuality,
                                                    const std::optional<float> &showResRing,
                                                    const std::optional<std::string> &color,
+                                                   const std::optional<bool> &showResEst,
                                                    Pistache::Http::ResponseWriter &response)  {
     int64_t image_id = id.value_or(ImageBuffer::MaxImage);
     PreviewImageSettings settings{};
@@ -485,7 +486,8 @@ void JFJochBrokerHttp::image_buffer_image_jpeg_get(const std::optional<int64_t>
     settings.show_user_mask = showUserMask.value_or(true);
     settings.show_roi = showRoi.value_or(false);
     settings.show_spots = showSpots.value_or(true);
-    settings.saturation_value = saturation.value_or(10);
+    settings.saturation_value = saturation;
+    settings.background_value = 0.0;
     settings.jpeg_quality = jpegQuality.value_or(100);
     settings.resolution_ring = showResRing;
     settings.scale = ConvertColorScale(color);

broker/JFJochBrokerHttp.h

@@ -147,6 +147,7 @@ class JFJochBrokerHttp : public org::openapitools::server::api::DefaultApi {
 
     void image_buffer_image_cbor_get(const std::optional<int64_t> &id,
                                      Pistache::Http::ResponseWriter &response) override;
+
     void image_buffer_image_jpeg_get(const std::optional<int64_t> &id,
                                      const std::optional<bool> &showUserMask,
                                      const std::optional<bool> &showRoi,
@@ -156,6 +157,7 @@ class JFJochBrokerHttp : public org::openapitools::server::api::DefaultApi {
                                      const std::optional<int64_t> &jpegQuality,
                                      const std::optional<float> &showResRing,
                                      const std::optional<std::string> &color,
+                                     const std::optional<bool> &showResEst,
                                      Pistache::Http::ResponseWriter &response) override;
 
     void image_buffer_image_tiff_get(const std::optional<int64_t> &id, Pistache::Http::ResponseWriter &response) override;

broker/gen/api/DefaultApi.cpp

@@ -1114,9 +1114,17 @@ void DefaultApi::image_buffer_image_jpeg_get_handler(const Pistache::Rest::Reque
             color = valueQuery_instance;
         }
     }
+    auto showResEstQuery = request.query().get("show_res_est");
+    std::optional<bool> showResEst;
+    if(showResEstQuery.has_value()){
+        bool valueQuery_instance;
+        if(fromStringValue(showResEstQuery.value(), valueQuery_instance)){
+            showResEst = valueQuery_instance;
+        }
+    }
     
     try {
-        this->image_buffer_image_jpeg_get(id, showUserMask, showRoi, showSpots, showBeamCenter, saturation, jpegQuality, showResRing, color, response);
+        this->image_buffer_image_jpeg_get(id, showUserMask, showRoi, showSpots, showBeamCenter, saturation, jpegQuality, showResRing, color, showResEst, response);
     } catch (Pistache::Http::HttpError &e) {
         response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
         return;

broker/gen/api/DefaultApi.h

@@ -462,11 +462,12 @@ private:
     /// <param name="showRoi">Show ROI areas on the image (optional, default to false)</param>
     /// <param name="showSpots">Show spot finding results on the image (optional, default to true)</param>
     /// <param name="showBeamCenter">Show beam center on the image (optional, default to true)</param>
-    /// <param name="saturation">Saturation value to set contrast in the preview image (optional, default to 10.0f)</param>
+    /// <param name="saturation">Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used (optional, default to 0.0f)</param>
     /// <param name="jpegQuality">Quality of JPEG image (100 - highest; 0 - lowest) (optional, default to 100L)</param>
     /// <param name="showResRing">Show resolution ring, provided in Angstrom (optional, default to 0.1f)</param>
     /// <param name="color">Color scale for preview image: 0 - indigo, 1 - viridis, 2 - B/W, 3 - heat (optional, default to &quot;indigo&quot;)</param>
-    virtual void image_buffer_image_jpeg_get(const std::optional<int64_t> &id, const std::optional<bool> &showUserMask, const std::optional<bool> &showRoi, const std::optional<bool> &showSpots, const std::optional<bool> &showBeamCenter, const std::optional<float> &saturation, const std::optional<int64_t> &jpegQuality, const std::optional<float> &showResRing, const std::optional<std::string> &color, Pistache::Http::ResponseWriter &response) = 0;
+    /// <param name="showResEst">Show resolution estimation as a ring (optional, default to false)</param>
+    virtual void image_buffer_image_jpeg_get(const std::optional<int64_t> &id, const std::optional<bool> &showUserMask, const std::optional<bool> &showRoi, const std::optional<bool> &showSpots, const std::optional<bool> &showBeamCenter, const std::optional<float> &saturation, const std::optional<int64_t> &jpegQuality, const std::optional<float> &showResRing, const std::optional<std::string> &color, const std::optional<bool> &showResEst, Pistache::Http::ResponseWriter &response) = 0;
     /// <summary>
     /// Get preview image in TIFF format
     /// </summary>

broker/jfjoch_api.yaml

@@ -143,16 +143,17 @@ components:
     saturation:
       in: query
       name: saturation
+      required: false
       schema:
         type: number
         format: float
-        default: 10
         minimum: -32767
         maximum: 32767
-      description: "Saturation value to set contrast in the preview image"
+      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
@@ -208,6 +209,13 @@ components:
         default: 0.1
         minimum: 0.1
         maximum: 100.0
+    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
@@ -3166,6 +3174,7 @@ paths:
         - $ref: '#/components/parameters/jpeg_quality'
         - $ref: '#/components/parameters/resolution_ring'
         - $ref: '#/components/parameters/color_scale'
+        - $ref: '#/components/parameters/resolution_estimate'
       responses:
         "200":
           description: Preview image

docs/python_client/docs/DefaultApi.md

@@ -2665,7 +2665,7 @@ No authorization required
 [[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)
 
 # **image_buffer_image_jpeg_get**
-> bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color)
+> bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
 
 Get preview image in JPEG format using custom settings
 
@@ -2693,14 +2693,15 @@ with jfjoch_client.ApiClient(configuration) as api_client:
     show_roi = False # bool | Show ROI areas on the image (optional) (default to False)
     show_spots = True # bool | Show spot finding results on the image (optional) (default to True)
     show_beam_center = True # bool | Show beam center on the image (optional) (default to True)
-    saturation = 10 # float | Saturation value to set contrast in the preview image (optional) (default to 10)
+    saturation = 3.4 # float | Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used (optional)
     jpeg_quality = 100 # int | Quality of JPEG image (100 - highest; 0 - lowest) (optional) (default to 100)
     show_res_ring = 0.1 # float | Show resolution ring, provided in Angstrom (optional) (default to 0.1)
     color = indigo # str | Color scale for preview image: 0 - indigo, 1 - viridis, 2 - B/W, 3 - heat (optional) (default to indigo)
+    show_res_est = False # bool | Show resolution estimation as a ring (optional) (default to False)
 
     try:
         # Get preview image in JPEG format using custom settings
-        api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color)
+        api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
         print("The response of DefaultApi->image_buffer_image_jpeg_get:\n")
         pprint(api_response)
     except Exception as e:
@@ -2719,10 +2720,11 @@ Name | Type | Description  | Notes
  **show_roi** | **bool**| Show ROI areas on the image | [optional] [default to False]
  **show_spots** | **bool**| Show spot finding results on the image | [optional] [default to True]
  **show_beam_center** | **bool**| Show beam center on the image | [optional] [default to True]
- **saturation** | **float**| Saturation value to set contrast in the preview image | [optional] [default to 10]
+ **saturation** | **float**| Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used | [optional] 
  **jpeg_quality** | **int**| Quality of JPEG image (100 - highest; 0 - lowest) | [optional] [default to 100]
  **show_res_ring** | **float**| Show resolution ring, provided in Angstrom | [optional] [default to 0.1]
  **color** | **str**| Color scale for preview image: 0 - indigo, 1 - viridis, 2 - B/W, 3 - heat | [optional] [default to indigo]
+ **show_res_est** | **bool**| Show resolution estimation as a ring | [optional] [default to False]
 
 ### Return type
 

frontend/package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.109",
+  "version": "1.0.0-rc.110",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "jungfraujoch-frontend",
-      "version": "1.0.0-rc.109",
+      "version": "1.0.0-rc.110",
       "license": "GPL-3.0",
       "dependencies": {
         "@emotion/react": "^11.10.4",

frontend/src/openapi/index.ts

@@ -54,6 +54,7 @@ export type { plot } from './models/plot';
 export { plot_type } from './models/plot_type';
 export { plot_unit_x } from './models/plot_unit_x';
 export type { plots } from './models/plots';
+export type { resolution_estimate } from './models/resolution_estimate';
 export type { resolution_ring } from './models/resolution_ring';
 export type { roi } from './models/roi';
 export type { roi_azim_list } from './models/roi_azim_list';

frontend/src/openapi/models/resolution_estimate.ts

@@ -0,0 +1,9 @@
+/* generated using openapi-typescript-codegen -- do no edit */
+/* istanbul ignore file */
+/* tslint:disable */
+/* eslint-disable */
+
+/**
+ * Show resolution estimation as a ring
+ */
+export type resolution_estimate = boolean;

frontend/src/openapi/models/saturation.ts

@@ -4,6 +4,6 @@
 /* eslint-disable */
 
 /**
- * Saturation value to set contrast in the preview image
+ * Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
  */
 export type saturation = number;

frontend/src/openapi/services/DefaultService.ts

@@ -1078,10 +1078,11 @@ export class DefaultService {
      * @param showRoi Show ROI areas on the image
      * @param showSpots Show spot finding results on the image
      * @param showBeamCenter Show beam center on the image
-     * @param saturation Saturation value to set contrast in the preview image
+     * @param saturation Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used
      * @param jpegQuality Quality of JPEG image (100 - highest; 0 - lowest)
      * @param showResRing Show resolution ring, provided in Angstrom
      * @param color Color scale for preview image: 0 - indigo, 1 - viridis, 2 - B/W, 3 - heat
+     * @param showResEst Show resolution estimation as a ring
      * @returns binary Preview image
      * @throws ApiError
      */
@@ -1091,10 +1092,11 @@ export class DefaultService {
         showRoi: boolean = false,
         showSpots: boolean = true,
         showBeamCenter: boolean = true,
-        saturation: number = 10,
+        saturation?: number,
         jpegQuality: number = 100,
         showResRing: number = 0.1,
         color: 'indigo' | 'viridis' | 'bw' | 'heat' = 'indigo',
+        showResEst: boolean = false,
     ): CancelablePromise<Blob> {
         return __request(OpenAPI, {
             method: 'GET',
@@ -1109,6 +1111,7 @@ export class DefaultService {
                 'jpeg_quality': jpegQuality,
                 'show_res_ring': showResRing,
                 'color': color,
+                'show_res_est': showResEst,
             },
             errors: {
                 400: `Input parsing or validation error`,

preview/PreviewImage.cpp

@@ -48,14 +48,46 @@ void PreviewImage::roi(std::vector<rgb> &ret, int64_t in_xpixel, int64_t in_ypix
 }
 
 template<class T>
-std::vector<rgb> PreviewImage::GenerateRGB(const uint8_t* value_8,
+std::vector<rgb> PreviewImage::GenerateRGB(const uint8_t *value_8,
                                            int64_t special_value_64,
+                                           int64_t sat_value_64,
                                            const ColorScale &scale,
-                                           const PreviewImageSettings& settings) const {
+                                           const PreviewImageSettings &settings) const {
     auto value = reinterpret_cast<const T *>(value_8);
     auto special_value = static_cast<T>(special_value_64);
 
-    std::vector<rgb> ret(xpixel*ypixel);
+    float background = settings.background_value.value_or(0.0);
+    float foreground;
+    if (settings.saturation_value.has_value())
+        foreground = settings.saturation_value.value();
+    else {
+        // Auto-contrast procedure
+        std::vector<int64_t> valid;
+        valid.reserve(xpixel * ypixel);
+        for (int i = 0; i < xpixel * ypixel; i++) {
+            if ((value[i] != special_value)
+                && (value[i] != sat_value_64)
+                && (mask[i] != MaskDet)
+                && (mask[i] != MaskGap)
+                && (!settings.show_user_mask || (mask[i] != MaskUsr)))
+                valid.push_back(static_cast<int64_t>(value[i]));
+        }
+
+        if (!valid.empty()) {
+            const size_t m = valid.size();
+            size_t ignore = std::max<size_t>(1, static_cast<size_t>(std::floor(m * auto_foreground_range)));
+            if (ignore >= m) ignore = m - 1; // ensure at least one value remains
+            const size_t rank = m - ignore - 1; // 0-based index for the desired value
+            std::nth_element(valid.begin(), valid.begin() + rank, valid.end());
+            foreground = static_cast<float>(valid[rank]);
+        } else {
+            // Fallback to something above background if no valid pixels remain
+            foreground = background + 1.0f;
+        }
+
+    }
+
+    std::vector<rgb> ret(xpixel * ypixel);
     for (int i = 0; i < xpixel*ypixel; i++) {
         if (mask[i] == MaskGap)
             ret[i] = scale.Apply(ColorScaleSpecial::Gap);
@@ -64,7 +96,7 @@ std::vector<rgb> PreviewImage::GenerateRGB(const uint8_t* value_8,
                  || (settings.show_user_mask && (mask[i] == MaskUsr))) {
             ret[i] = scale.Apply(ColorScaleSpecial::BadPixel);
         } else
-            ret[i] = scale.Apply(value[i], 0.0, settings.saturation_value);;
+            ret[i] = scale.Apply(value[i], background, foreground);
     }
     return ret;
 }
@@ -214,22 +246,22 @@ std::vector<rgb> PreviewImage::GenerateRGB(const PreviewImageSettings &settings,
 
         switch (msg.image.GetMode()) {
             case CompressedImageMode::Int8:
-                v = GenerateRGB<int8_t>(image_ptr, INT8_MIN, scale, settings);
+                v = GenerateRGB<int8_t>(image_ptr, INT8_MIN, INT8_MAX, scale, settings);
                 break;
             case CompressedImageMode::Int16:
-                v = GenerateRGB<int16_t>(image_ptr, INT16_MIN, scale, settings);
+                v = GenerateRGB<int16_t>(image_ptr, INT16_MIN, INT16_MAX, scale, settings);
                 break;
             case CompressedImageMode::Int32:
-                v = GenerateRGB<int32_t>(image_ptr, INT32_MIN, scale, settings);
+                v = GenerateRGB<int32_t>(image_ptr, INT32_MIN, INT32_MAX, scale, settings);
                 break;
             case CompressedImageMode::Uint8:
-                v = GenerateRGB<uint8_t>(image_ptr,UINT8_MAX, scale, settings);
+                v = GenerateRGB<uint8_t>(image_ptr,UINT8_MAX, UINT8_MAX, scale, settings);
                 break;
             case CompressedImageMode::Uint16:
-                v = GenerateRGB<uint16_t>(image_ptr,UINT16_MAX, scale, settings);
+                v = GenerateRGB<uint16_t>(image_ptr,UINT16_MAX, UINT16_MAX, scale, settings);
                 break;
             case CompressedImageMode::Uint32:
-                v = GenerateRGB<uint32_t>(image_ptr,UINT16_MAX, scale, settings);
+                v = GenerateRGB<uint32_t>(image_ptr,UINT32_MAX, UINT32_MAX, scale, settings);
                 break;
             default:
                 throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Mode not supported");

preview/PreviewImage.h

@@ -16,7 +16,8 @@
 enum class PreviewImageFormat {JPEG, TIFF};
 
 struct PreviewImageSettings {
-    float saturation_value = 10;
+    std::optional<float> saturation_value = 10;
+    std::optional<float> background_value = 0;
     int64_t jpeg_quality = 70;
     bool show_beam_center = true;
     bool show_spots = true;
@@ -46,9 +47,12 @@ class PreviewImage {
     constexpr static uint8_t MaskUsr = 2;
     constexpr static uint8_t MaskDet = 3;
 
+    constexpr static float auto_foreground_range = 0.001f;
+
     template<class T>
     std::vector<rgb> GenerateRGB(const uint8_t* value,
                                  int64_t special_value,
+                                 int64_t sat_value,
                                  const ColorScale &scale,
                                  const PreviewImageSettings& settings) const;
     std::vector<rgb> GenerateRGB(const PreviewImageSettings& settings, const DataMessage &msg) const;

tests/JFJochReceiverProcessingTest.cpp

@@ -995,7 +995,6 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
 
     std::string jpeg;
     PreviewImageSettings jpeg_settings{
-            .saturation_value = 10,
             .jpeg_quality = 100,
             .show_spots = true
     };