Merge pull request #74 from BoostV/73-plot-uncertainty-of-individual-experiment-plot

73 plot uncertainty of individual experiment plot

Author: langdal

optimizerapi/optimizer.py

@@ -111,12 +111,13 @@ def do_run_work(body) -> dict:
 
 def __handle_run(body) -> dict:
     """ "Handle the run request"""
-    # print("Receive: " + str(body))
     data = [(run["xi"], run["yi"]) for run in body["data"]]
     cfg = body["optimizerConfig"]
     constraints = cfg["constraints"] if "constraints" in cfg else []
     extras = body["extras"] if "extras" in body else {}
-    print("Received extras " + str(extras))
+    use_actual_measurement_histogram = json.loads(
+        extras.get("useActualMeasurementHistogram", "true").lower()
+    )
     space = [
         (
             convert_number_type(x["from"], x["type"]),
@@ -159,6 +160,9 @@ def __handle_run(body) -> dict:
             Yi = [elm[0] for elm in Yi]
         result = optimizer.tell(Xi, Yi)
         if n_objectives == 1:
+            if use_actual_measurement_histogram:
+                optimizer.add_modelled_noise()
+                result = optimizer.get_result()
             result = [result]
     else:
         result = []
@@ -227,7 +231,7 @@ def process_result(result, optimizer, dimensions, cfg, extras, data, space):
     # as "None" at the moment.
     graph_format = extras.get("graphFormat", "png")
     max_quality = int(extras.get("maxQuality", "5"))
-    graphs_to_return = extras.get("graphs", ['objective', 'convergence', 'pareto'])
+    graphs_to_return = extras.get("graphs", ["objective", "convergence", "pareto"])
 
     objective_pars = extras.get("objectivePars", "result")
 
@@ -251,19 +255,21 @@ def process_result(result, optimizer, dimensions, cfg, extras, data, space):
         result_details["models"] = [process_model(model, optimizer) for model in result]
         if graph_format == "png":
             for idx, model in enumerate(result):
-                if 'single' in graphs_to_return:
+                if "single" in graphs_to_return:
                     bb_plots = plot_brownie_bee(model, max_quality=max_quality)
                     for i, plot in enumerate(bb_plots):
                         pic_io_bytes = io.BytesIO()
                         plot.savefig(pic_io_bytes, format="png")
                         pic_io_bytes.seek(0)
                         pic_hash = base64.b64encode(pic_io_bytes.read())
-                        plots.append({"id": f"single_{idx}_{i}", "plot": str(pic_hash, "utf-8")})
-                if 'convergence' in graphs_to_return:
+                        plots.append(
+                            {"id": f"single_{idx}_{i}", "plot": str(pic_hash, "utf-8")}
+                        )
+                if "convergence" in graphs_to_return:
                     plot_convergence(model)
                     add_plot(plots, f"convergence_{idx}")
 
-                if 'objective' in graphs_to_return:
+                if "objective" in graphs_to_return:
                     plot_objective(
                         model,
                         dimensions=dimensions,
@@ -279,7 +285,7 @@ def process_result(result, optimizer, dimensions, cfg, extras, data, space):
                     round_to_length_scales(minimum[0], optimizer.space),
                     minimum[1],
                 ]
-            elif 'pareto' in graphs_to_return:
+            elif "pareto" in graphs_to_return:
                 plot_Pareto(optimizer)
                 add_plot(plots, "pareto")
 

requirements-freeze.txt

@@ -1,23 +1,35 @@
+a2wsgi==1.7.0
+anyio==3.6.2
+asgiref==3.6.0
 async-timeout==4.0.2
 attrs==23.1.0
+black==23.3.0
 bokeh==2.4.3
 certifi==2022.12.7
 cffi==1.15.1
 charset-normalizer==3.1.0
 click==8.1.3
 clickclick==20.10.2
+colorama==0.4.6
 connexion==2.14.2
 cryptography==3.4.7
 cycler==0.11.0
 deap==1.3.3
 deprecation==2.1.0
+docopt==0.6.2
 ecdsa==0.18.0
+flake8==6.1.0
 Flask==2.2.3
 Flask-Cors==3.0.10
 fonttools==4.39.3
+h11==0.14.0
+httpcore==0.16.3
+httptools==0.5.0
+httpx==0.23.3
 idna==3.4
 importlib-metadata==6.4.1
 inflection==0.5.1
+iniconfig==2.0.0
 itsdangerous==2.1.2
 Jinja2==3.1.2
 joblib==1.2.0
@@ -26,31 +38,54 @@ jsonschema==4.15.0
 kiwisolver==1.4.4
 MarkupSafe==2.1.2
 matplotlib==3.5.3
+mccabe==0.7.0
+mypy-extensions==1.0.0
 numpy==1.23.3
 packaging==23.1
+pathspec==0.11.1
 Pillow==9.5.0
-ProcessOptimizer[browniebee]==0.8.0
+platformdirs==3.5.0
+pluggy==0.13.1
+ProcessOptimizer[browniebee]==0.8.1
+py==1.11.0
+py-swagger-ui==1.1.0
 pyasn1==0.4.8
+pycodestyle==2.11.0
 pycparser==2.21
+pyflakes==3.1.0
 pyparsing==3.0.9
 pyrsistent==0.19.3
+pytest==6.2.2
+pytest-watch==4.2.0
 python-dateutil==2.8.2
+python-dotenv==1.0.0
 python-jose==3.3.0
 python-keycloak==2.13.2
+python-multipart==0.0.6
 PyYAML==6.0
 redis==4.5.4
 requests==2.28.2
 requests-toolbelt==0.10.1
+rfc3986==1.5.0
 rq==1.10.0
 rsa==4.9
 scikit-learn==1.1.2
 scipy==1.9.1
 six==1.16.0
+sniffio==1.3.0
+starlette==0.25.0
 swagger-ui-bundle==0.0.9
 threadpoolctl==3.1.0
+toml==0.10.2
+tomli==2.0.1
 tornado==6.2
 typing_extensions==4.5.0
 urllib3==1.26.15
+uvicorn==0.17.6
+uvloop==0.17.0
 waitress==2.1.2
+watchdog==3.0.0
+watchgod==0.8.2
+websockets==11.0.2
 Werkzeug==2.2.3
 zipp==3.15.0

requirements.txt

@@ -3,7 +3,7 @@ connexion[swagger-ui]
 python-keycloak==2.13.2
 Flask==2.2.3
 Flask-Cors==3.0.10
-ProcessOptimizer[browniebee]==0.8.0
+ProcessOptimizer[browniebee]==0.8.1
 json-tricks==3.15.5
 jsonschema==4.15.0
 cryptography==3.4.7