🧪Project API Tryout - Fluorescence example 🚧

.gitignore

@@ -138,3 +138,5 @@ plot_results
 
 # DOAS data file
 !pyglotaran_examples/ex_doas_beta/data/2008Polli_betacar_chex_sim.nc
+
+pyglotaran_examples/study_fluorescence/results/*

pyglotaran_examples/study_fluorescence/models/parameters.yaml → pyglotaran_examples/study_fluorescence/parameters/parameters.yml

@@ -13,4 +13,4 @@ kinetic:
   - 0.07
   - 0.02
   - 0.00016
-  - {non-negative: true}
+  # - {non-negative: true}

pyglotaran_examples/study_fluorescence/project.gta

@@ -0,0 +1 @@
+version: 0.7.0.dev0

pyglotaran_examples/study_fluorescence/scheme.yml

@@ -0,0 +1,13 @@
+model: models/model.yml
+parameters: parameters/parameters.yml
+data:
+  dataset1: dataset1.nc
+clp_link_tolerance: 0.0
+clp_link_method: nearest
+maximum_number_function_evaluations: null
+add_svd: true
+ftol: 1e-08
+gtol: 1e-08
+xtol: 1e-08
+optimization_method: TrustRegionReflection
+result_path: null

pyglotaran_examples/study_fluorescence/target_analysis_script.py

@@ -14,10 +14,10 @@
 from pyglotaran_extras.plotting.plot_overview import plot_overview
 from pyglotaran_extras.plotting.style import PlotStyle
 
-GLOBAL_MODEL = "models/model.yaml"
-GLOBAL_PARAMS = "models/parameters.yaml"
+GLOBAL_MODEL = "models/model.yml"
+GLOBAL_PARAMS = "parameters/parameters.yml"
 TARGET_MODEL = "models/model-target.yaml"
-TARGET_PARAMS = "models/parameters-target.yaml"
+TARGET_PARAMS = "parameters/parameters-target.yaml"
 SKIP_FIT = False
 
 # %%
@@ -26,7 +26,7 @@
 
 
 # %%
-data_path = script_folder.joinpath("data/data.ascii")
+data_path = script_folder.joinpath("data/dataset1.ascii")
 # model_path = script_folder.joinpath(GLOBAL_MODEL)
 # parameter_path = script_folder.joinpath(GLOBAL_PARAMS)
 model_path = script_folder.joinpath(TARGET_MODEL)

pyglotaran_examples/study_fluorescence/tryout_project_api.py

@@ -0,0 +1,36 @@
+from pathlib import Path
+from timeit import default_timer as timer
+
+import matplotlib.pyplot as plt  # 3.3 or higher
+from glotaran.project.project import Project
+from pyglotaran_extras.plotting.plot_overview import plot_overview
+
+if __name__ == "__main__":
+    project_file = Path(".") / "project.gta"
+    project_folder = project_file.parent
+    project = Project.open(project_file)
+
+    project.load_data("dataset1.ascii")
+    # Would prefer to decouple dataset label and filename
+
+    start = timer()
+    project.optimize(
+        # model_name="model.yml", #  note if you use 'model' it will pick the wrong file
+        # parameters_name="parameters.yml",
+        model_name="model-target.yaml",
+        parameters_name="parameters-target.yaml",
+        maximum_number_function_evaluations=100,
+        result_name="dummy",
+    )
+    end = timer()
+    print(f"Total time: {end - start}")
+
+    result = project.load_latest_result("dummy")
+
+    print(result.markdown(True))
+
+    res = result.data["dataset1"]
+    print(res)
+
+    fig, _ = plot_overview(result, linlog=False, figure_only=False)
+    plt.show(block=True)