- add example for steady state

copasi · Feb 2, 2023 · 1a00bb7 · 1a00bb7
1 parent 3dd1e77
commit 1a00bb7
Showing 1 changed file with 69 additions and 9 deletions.
diff --git a/docs/notebooks/Working_with_Reports.ipynb b/docs/notebooks/Working_with_Reports.ipynb
@@ -254,6 +254,66 @@
     "the value in `print_headers` indicates, whether the name of the elements will be printed in the header column. "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "609f5f04",
+   "metadata": {},
+   "source": [
+    "using the `table` element directly, does only work for tasks that generate output *during* the execution of the task, as in the time course example above. Other tasks, such as steady state computation only provide results *after* the task has completed. In the following we add a report for the steady state concentration (and rate of X). We use the function `wrap_copasi_string`, to indicate that we want to have the literal string `[X]` in the header, rather than the initial concentration: "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "18b5399b",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<CReportDefinition \"X Steady-State\">"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "add_report('X Steady-State', task=T.STEADY_STATE, \n",
+    "           header=[wrap_copasi_string('[X]'), wrap_copasi_string('X.Rate')], \n",
+    "           footer=['[X]', 'X.Rate'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "69b29e21",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'name': 'X Steady-State',\n",
+       " 'separator': '\\t',\n",
+       " 'precision': 6,\n",
+       " 'task': 'Steady-State',\n",
+       " 'comment': '',\n",
+       " 'is_table': False,\n",
+       " 'header': ['String=\\\\[X\\\\]', 'String=X.Rate'],\n",
+       " 'body': [],\n",
+       " 'footer': ['[X]', 'X.Rate']}"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "get_report_dict('X Steady-State')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "6742259a",
@@ -265,7 +325,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 10,
    "id": "8dbe7023",
    "metadata": {},
    "outputs": [],
@@ -275,7 +335,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 11,
    "id": "cbb20d4c",
    "metadata": {},
    "outputs": [
@@ -292,7 +352,7 @@
        " 'table': ['Time', '[X]', 'X.Rate']}"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -320,7 +380,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 12,
    "id": "3d916516",
    "metadata": {},
    "outputs": [],
@@ -338,7 +398,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 13,
    "id": "251fdf2a",
    "metadata": {},
    "outputs": [],
@@ -358,7 +418,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 14,
    "id": "1b37f539",
    "metadata": {},
    "outputs": [
@@ -368,7 +428,7 @@
        "'X Time-Course'"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -380,7 +440,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -394,7 +454,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,