♻️ Converted target_rcg_compare to project API

glotaran · Feb 27, 2023 · 01ba768 · 01ba768
1 parent 0701661
commit 01ba768
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Showing 5 changed files with 43 additions and 32 deletions.
diff --git a/rc/models/model_target_noRP_rcg_refine.yml → rc/models/target_noRP_rcg_refine.yml b/rc/models/model_target_noRP_rcg_refine.yml → rc/models/target_noRP_rcg_refine.yml
diff --git a/rc/models/model_target_rcg_refine.yml → rc/models/target_rcg_refine.yml b/rc/models/model_target_rcg_refine.yml → rc/models/target_rcg_refine.yml
diff --git a/...ameters_target_rcg_gcrcg_rcgcr_refine.yml → rc/parameters/target_noRP_rcg_refine.yml b/...ameters_target_rcg_gcrcg_rcgcr_refine.yml → rc/parameters/target_noRP_rcg_refine.yml
diff --git a/rc/models/parameters_target_rcg_refine.yml → rc/parameters/target_rcg_refine.yml b/rc/models/parameters_target_rcg_refine.yml → rc/parameters/target_rcg_refine.yml
diff --git a/rc/target_rcg_compare_part2.ipynb b/rc/target_rcg_compare_part2.ipynb
@@ -44,6 +44,35 @@
     "# Inspect experimental data\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from glotaran.project import Project\n",
+    "\n",
+    "project = Project.open(\"\")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grga.ascii\", dataset_name=\"tas_rcg_dcm\", ignore_existing=True\n",
+    ")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grgc.ascii\", dataset_name=\"guide_rcg_r1\", ignore_existing=True\n",
+    ")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grgd.ascii\", dataset_name=\"guide_rcg_r2\", ignore_existing=True\n",
+    ")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grge.ascii\", dataset_name=\"guide_rcg_r3\", ignore_existing=True\n",
+    ")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grgf.ascii\", dataset_name=\"guide_rcg_r4\", ignore_existing=True\n",
+    ")\n",
+    "project.import_data(\n",
+    "    \"measured_data/Krg_grgg.ascii\", dataset_name=\"guide_rcg_g\", ignore_existing=True\n",
+    ")"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -87,7 +116,7 @@
     "    # \"guide_rcgcr_r4\": \"data/Krg_grgf.ascii\",\n",
     "}\n",
     "\n",
-    "plot_data_overview(experiment_data[\"tas_rcg_dcm\"], linlog=True, linthresh=1)"
+    "plot_data_overview(project.data[\"tas_rcg_dcm\"], linlog=True, linthresh=1);"
    ]
   },
   {
@@ -110,10 +139,7 @@
    },
    "outputs": [],
    "source": [
-    "# from glotaran.utils.ipython import display_file\n",
-    "\n",
-    "model_path = \"models/model_target_rcg_refine.yml\"\n",
-    "# display_file(model_path, syntax=\"yaml\")"
+    "# project.show_model_definition(\"target_rcg_refine\")"
    ]
   },
   {
@@ -138,8 +164,7 @@
    },
    "outputs": [],
    "source": [
-    "parameters_file_path = \"models/parameters_target_rcg_refine.yml\"\n",
-    "# display_file(parameters_file_path, syntax=\"yaml\")"
+    "# project.show_parameters_definition(\"target_rcg_refine\")"
    ]
   },
   {
@@ -175,17 +200,12 @@
    },
    "outputs": [],
    "source": [
-    "from glotaran.optimization.optimize import optimize\n",
-    "from glotaran.project.scheme import Scheme\n",
-    "\n",
-    "scheme = Scheme(\n",
-    "    model_path,\n",
-    "    parameters_file_path,\n",
-    "    experiment_data,\n",
+    "result = project.optimize(\n",
+    "    model_name=\"target_rcg_refine\",\n",
+    "    parameters_name=\"target_rcg_refine\",\n",
     "    clp_link_tolerance=1.9,\n",
     "    maximum_number_function_evaluations=1,\n",
-    ")\n",
-    "result = optimize(scheme)"
+    ")"
    ]
   },
   {
@@ -337,7 +357,6 @@
    },
    "outputs": [],
    "source": [
-    "\n",
     "from pyglotaran_extras.plotting.style import PlotStyle\n",
     "\n",
     "# fig, ax = plt.subplots(1, 1, figsize=(15, 7))\n",
@@ -494,21 +513,12 @@
    },
    "outputs": [],
    "source": [
-    "from glotaran.optimization.optimize import optimize\n",
-    "from glotaran.project.scheme import Scheme\n",
-    "\n",
-    "model_noRP_path = \"models/model_target_noRP_rcg_refine.yml\"\n",
-    "parameters_noRP_file_path = \"models/parameters_target_noRP_rcg_refine.yml\"\n",
-    "\n",
-    "\n",
-    "scheme_noRP = Scheme(\n",
-    "    model_noRP_path,\n",
-    "    parameters_noRP_file_path,\n",
-    "    experiment_data,\n",
+    "result_noRP = project.optimize(\n",
+    "    model_name=\"target_noRP_rcg_refine\",\n",
+    "    parameters_name=\"target_noRP_rcg_refine\",\n",
     "    clp_link_tolerance=1.9,\n",
-    "    maximum_number_function_evaluations=1,\n",
-    ")\n",
-    "result_noRP = optimize(scheme_noRP)"
+    "    maximum_number_function_evaluations=7,\n",
+    ")"
    ]
   },
   {
@@ -593,7 +603,8 @@
     "axes[1][0].annotate(\"C\", xy=(0.01, 0.92), xycoords=\"axes fraction\", fontsize=16)\n",
     "axes[1][1].annotate(\"D\", xy=(0.01, 0.92), xycoords=\"axes fraction\", fontsize=16)\n",
     "for ax in axes[0:3, 0:3].flatten():\n",
-    "    ax.axhline(0, color=\"k\", linewidth=1)"
+    "    ax.axhline(0, color=\"k\", linewidth=1)\n",
+    "fig.tight_layout()"
    ]
   }
  ],