diff --git a/jupyter_notebooks/diagrams.ipynb b/jupyter_notebooks/diagrams.ipynb
index 8fd65bc..2c4e407 100644
--- a/jupyter_notebooks/diagrams.ipynb
+++ b/jupyter_notebooks/diagrams.ipynb
@@ -503,7 +503,7 @@
},
{
"cell_type": "code",
- "execution_count": 29,
+ "execution_count": 66,
"id": "8166389b-a006-490a-8e84-9e67e49591ed",
"metadata": {},
"outputs": [
@@ -511,7 +511,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Initializing experiment tumor_tcell_20231026.220231\n"
+ "Initializing experiment tumor_tcell_20231026.222910\n"
]
},
{
@@ -569,7 +569,7 @@
},
{
"cell_type": "code",
- "execution_count": 30,
+ "execution_count": 67,
"id": "589648aa-b5b8-497c-b937-366c87dae3de",
"metadata": {},
"outputs": [],
@@ -599,19 +599,10 @@
},
{
"cell_type": "code",
- "execution_count": 49,
+ "execution_count": 68,
"id": "10df1f44-fd56-46b9-8806-a959c071978f",
"metadata": {},
"outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "node ('agents',) not in graph\n",
- "node ('fields',) not in graph\n",
- "node ('dimensions',) not in graph\n"
- ]
- },
{
"data": {
"image/svg+xml": [
@@ -621,273 +612,276 @@
"\n",
"\n",
- "\n"
],
"text/plain": [
- ""
+ ""
]
},
- "execution_count": 35,
+ "execution_count": 72,
"metadata": {},
"output_type": "execute_result"
}
@@ -2040,7 +2032,7 @@
},
{
"cell_type": "code",
- "execution_count": 36,
+ "execution_count": 83,
"id": "b759be45-60a0-47b6-8622-571e0af6f18f",
"metadata": {},
"outputs": [
@@ -2053,106 +2045,99 @@
"\n",
"\n",
- "\n",
- "\n",
+ "\n",
+ "\n",
"bigraph\n",
- "\n",
+ "\n",
"\n",
"\n",
"('agents',)\n",
- "\n",
- "agents\n",
+ "\n",
+ "agents\n",
"\n",
"\n",
"\n",
"('agents', 't_cell')\n",
- "\n",
- "t_cell\n",
+ "\n",
+ "t_cell\n",
"\n",
"\n",
"\n",
"('agents',)->('agents', 't_cell')\n",
- "\n",
+ "\n",
"\n",
- "\n",
- "\n",
- "('fields',)\n",
- "\n",
- "fields\n",
- "\n",
- "\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 'division')\n",
- "\n",
- "division\n",
+ "\n",
+ "division\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents',)->('agents', 't_cell', 'division')\n",
- "\n",
- "\n",
- "agents\n",
+ "\n",
+ "\n",
+ "agents\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 'death')\n",
- "\n",
- "death\n",
+ "\n",
+ "death\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents',)->('agents', 't_cell', 'death')\n",
- "\n",
- "\n",
- "agents\n",
+ "\n",
+ "\n",
+ "agents\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')\n",
- "\n",
- "boundary\n",
+ "\n",
+ "boundary\n",
"\n",
"\n",
"\n",
"('agents', 't_cell')->('agents', 't_cell', 'boundary')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'neighbors')\n",
- "\n",
- "neighbors\n",
+ "\n",
+ "neighbors\n",
"\n",
"\n",
"\n",
"('agents', 't_cell')->('agents', 't_cell', 'neighbors')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'internal')\n",
- "\n",
- "internal\n",
+ "\n",
+ "internal\n",
"\n",
"\n",
"\n",
"('agents', 't_cell')->('agents', 't_cell', 'internal')\n",
- "\n",
+ "\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 't_cell')\n",
- "\n",
- "t_cell\n",
+ "\n",
+ "t_cell\n",
"\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 'local_field')\n",
- "\n",
- "local_field\n",
+ "\n",
+ "local_field\n",
"\n",
"\n",
"\n",
@@ -2160,172 +2145,170 @@
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'death')\n",
- "\n",
- "death\n",
+ "\n",
+ "death\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'death')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'location')\n",
- "\n",
- "location\n",
+ "\n",
+ "location\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'location')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'exchange')\n",
- "\n",
- "exchange\n",
+ "\n",
+ "exchange\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'exchange')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'mass')\n",
- "\n",
- "mass\n",
+ "\n",
+ "mass\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'mass')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'diameter')\n",
- "\n",
- "diameter\n",
+ "\n",
+ "diameter\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'diameter')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'velocity')\n",
- "\n",
- "velocity\n",
+ "\n",
+ "velocity\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'boundary', 'velocity')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 't_cell')\n",
- "\n",
- "\n",
- "boundary\n",
+ "\n",
+ "\n",
+ "boundary\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 't_cell')\n",
- "\n",
- "\n",
- "globals\n",
+ "\n",
+ "\n",
+ "globals\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 'boundary')->('agents', 't_cell', 'division')\n",
- "\n",
- "\n",
- "global\n",
+ "\n",
+ "\n",
+ "global\n",
"\n",
"\n",
- "\n",
+ "\n",
"('agents', 't_cell', 'boundary', 'death')->('agents', 't_cell', 'death')\n",
- "\n",
- "\n",
- "trigger\n",
+ "\n",
+ "\n",
+ "trigger\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'location')->('agents', 't_cell', 'local_field')\n",
- "\n",
- "\n",
- "location\n",
+ "\n",
+ "\n",
+ "location\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'boundary', 'exchange')->('agents', 't_cell', 'local_field')\n",
- "\n",
- "\n",
- "exchanges\n",
+ "\n",
+ "\n",
+ "exchanges\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'neighbors')->('agents', 't_cell', 't_cell')\n",
- "\n",
- "\n",
- "neighbors\n",
+ "\n",
+ "\n",
+ "neighbors\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'internal', 'cell_state')\n",
- "\n",
- "cell_state\n",
+ "\n",
+ "cell_state\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'internal')->('agents', 't_cell', 'internal', 'cell_state')\n",
- "\n",
+ "\n",
"\n",
"\n",
"\n",
"('agents', 't_cell', 'internal')->('agents', 't_cell', 't_cell')\n",
- "\n",
- "\n",
- "internal\n",
+ "\n",
+ "\n",
+ "internal\n",
"\n",
- "\n",
- "\n",
- "('dimensions',)\n",
- "\n",
- "dimensions\n",
- "\n",
- "\n",
- "\n",
- "\n",
- "('fields',)->('agents', 't_cell', 'local_field')\n",
- "\n",
- "\n",
- "fields\n",
+ "\n",
+ "\n",
+ "\n",
+ "('agents', 't_cell', 'local_field', 'fields')->('agents', 't_cell', 'local_field')\n",
+ "\n",
+ "\n",
+ "fields\n",
"\n",
- "\n",
- "\n",
- "('dimensions',)->('agents', 't_cell', 'local_field')\n",
- "\n",
- "\n",
- "dimensions\n",
+ "\n",
+ "\n",
+ "\n",
+ "('agents', 't_cell', 'local_field', 'dimensions')->('agents', 't_cell', 'local_field')\n",
+ "\n",
+ "\n",
+ "dimensions\n",
"\n",
"\n",
"\n"
],
"text/plain": [
- ""
+ ""
]
},
- "execution_count": 36,
+ "execution_count": 83,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "node_groups = [[('agents',), ('fields',), ('dimensions',)]]\n",
- "tcell0 = tumor_agents_spec['tcell_0']\n",
+ "node_groups = [[('agents',)]]\n",
+ "tcell0 = copy.deepcopy(tumor_agents_spec['tcell_0'])\n",
+ "tcell0['local_field']['_ports'] = {'fields': '', 'dimensions': '', 'location': '', 'exchanges': ''}\n",
+ "del tcell0['local_field']['wires']['fields']\n",
+ "del tcell0['local_field']['wires']['dimensions']\n",
"\n",
"internal_spec = {'cell_state': {}}\n",
"boundary_spec = {'mass': {}, 'diameter': {}, 'velocity': {}}\n",
@@ -2333,6 +2316,7 @@
"tcell0['internal'].update(internal_spec)\n",
"\n",
"nodec1 = {\n",
+ " ('agents',): c2,\n",
" ('agents', 't_cell',): c3,\n",
" ('agents', 't_cell', 'boundary',): c4,\n",
" ('agents', 't_cell', 'internal',): c4,\n",
@@ -2342,13 +2326,14 @@
" ('agents', 't_cell', 't_cell'): 'red',\n",
"}\n",
"\n",
- "plot_bigraph({'agents': {'t_cell': tcell0}, 'fields': {}, 'dimensions': {}}, \n",
+ "plot_bigraph({'agents': {'t_cell': tcell0}}, \n",
" node_groups=node_groups,\n",
- " node_fill_colors={**nodec, **nodec1},\n",
+ " node_fill_colors={**nodec1},\n",
" node_border_colors=node_border_colors,\n",
" **plot_settings,\n",
" filename='tcell_composite',\n",
" remove_process_place_edges=True,\n",
+ " # **{'out_dir': 'out','dpi': '250'}\n",
" )"
]
},