🩹 Refine ex_spectral_constraints notbook to generate same files as sc…

…ript
glotaran · Jun 8, 2024 · 12a2b40 · 12a2b40
1 parent c644714
commit 12a2b40
Show file tree

Hide file tree

Showing 2 changed files with 48 additions and 19 deletions.
diff --git a/pyglotaran_examples/ex_spectral_constraints/ex_spectral_constraints.ipynb b/pyglotaran_examples/ex_spectral_constraints/ex_spectral_constraints.ipynb
@@ -56,10 +56,10 @@
     ")\n",
     "\n",
     "# optimization with first scheme\n",
-    "result = optimize(scheme_no_penalties)\n",
+    "result_no_penalties_first_run = optimize(scheme_no_penalties)\n",
     "# optimization with second scheme,\n",
     "# where we change the maximum number of function evaluations\n",
-    "scheme2 = result.get_scheme()\n",
+    "scheme2 = result_no_penalties_first_run.get_scheme()\n",
     "scheme2.maximum_number_function_evaluations = 2\n",
     "result_no_penalties = optimize(scheme2)"
    ]
@@ -84,8 +84,14 @@
     "from glotaran.io import save_result\n",
     "\n",
     "base_results_folder, _ = setup_case_study(output_folder_name=\"pyglotaran_examples_results\")\n",
-    "results_folder = base_results_folder / \"no_penalties\"\n",
-    "save_result(result_no_penalties, results_folder / \"result.yml\", allow_overwrite=True)"
+    "save_result(\n",
+    "    result_no_penalties_first_run,\n",
+    "    base_results_folder / \"no_penalties_first_run/result.yml\",\n",
+    "    allow_overwrite=True,\n",
+    ")\n",
+    "save_result(\n",
+    "    result_no_penalties, base_results_folder / \"no_penalties/result.yml\", allow_overwrite=True\n",
+    ");"
    ]
   },
   {
@@ -97,6 +103,7 @@
    "source": [
     "from pyglotaran_extras.plotting.plot_overview import plot_simple_overview\n",
     "\n",
+    "plot_simple_overview(result_no_penalties_first_run.data[\"dataset1\"])\n",
     "plot_simple_overview(result_no_penalties.data[\"dataset1\"]);"
    ]
   },
@@ -132,43 +139,65 @@
     "    maximum_number_function_evaluations=7,\n",
     ")\n",
     "\n",
-    "result_equal_area = optimize(scheme_equal_area)"
+    "result_equal_area_first_run = optimize(scheme_equal_area)"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "id": "9",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "#### Plotting"
+    "save_result(\n",
+    "    result_equal_area_first_run,\n",
+    "    base_results_folder / \"with_penalties_first_run/result.yml\",\n",
+    "    allow_overwrite=True,\n",
+    ");"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "10",
+   "metadata": {},
+   "source": [
+    "#### Run again with results from first run and save"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyglotaran_extras.plotting.plot_overview import plot_simple_overview\n",
-    "\n",
-    "plot_simple_overview(result_equal_area.data[\"dataset1\"]);"
+    "result_equal_area = optimize(result_equal_area_first_run.get_scheme())\n",
+    "save_result(\n",
+    "    result_equal_area,\n",
+    "    base_results_folder / \"with_penalties/result.yml\",\n",
+    "    allow_overwrite=True,\n",
+    ");"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "#### Plotting"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyglotaran_extras.io import setup_case_study\n",
-    "\n",
-    "from glotaran.io import save_result\n",
+    "from pyglotaran_extras.plotting.plot_overview import plot_simple_overview\n",
     "\n",
-    "base_results_folder, _ = setup_case_study(output_folder_name=\"pyglotaran_examples_results\")\n",
-    "results_folder = base_results_folder / \"with_penalties_first_run\"\n",
-    "save_result(result_equal_area, results_folder / \"result.yml\", allow_overwrite=True)"
+    "plot_simple_overview(result_equal_area_first_run.data[\"dataset1\"])\n",
+    "plot_simple_overview(result_equal_area.data[\"dataset1\"]);"
    ]
   }
  ],

diff --git a/pyglotaran_examples/ex_spectral_constraints/models/model_equal_area_penalties.yml b/pyglotaran_examples/ex_spectral_constraints/models/model_equal_area_penalties.yml
@@ -27,7 +27,7 @@ irf:
     center: irf.center
     width: irf.width
 
-clp_area_penalties:
+clp_penalties:
   - type: equal_area
     source: s2
     source_intervals: [[0, 1000]]