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Update/visualise #5

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merged 3 commits into from
Mar 7, 2023
Merged

Update/visualise #5

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6155a8a
update vis
srmnitc Mar 7, 2023
49d9a0e
update env
srmnitc Mar 7, 2023
6d03286
fix visualisation
srmnitc Mar 7, 2023
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1 change: 1 addition & 0 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,4 @@ dependencies:
- python-graphviz
- pyyaml
- ase
- ipycytoscape
63 changes: 31 additions & 32 deletions example.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -178,29 +178,6 @@
"g = StructureGraph()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "e7e17888-8da4-4618-9eb9-c599a83ababf",
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"<Graph identifier=N304404e3864e4aef8d79731c1ae06af1 (<class 'rdflib.graph.Graph'>)>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"g.graph.parse(\"pyscal_rdf/data/cmso.owl\", format='xml')"
]
},
{
"cell_type": "markdown",
"id": "0065555c-d343-4d1b-a05a-69ddac61a4c5",
Expand All @@ -211,39 +188,61 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 7,
"id": "3c50dba0-50a6-436f-9044-9105d93a6cb1",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"g.add_structure_to_graph(struct_l12)\n",
"g.add_structure_to_graph(struct_Fe)\n",
"g.add_structure_to_graph(struct_Si)"
"g.add_structure_to_graph(struct_l12)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "3ee82cb2-7566-4749-963c-80f2040361d4",
"execution_count": 12,
"id": "43e6adf0-b33d-4d86-84b1-2a40cf1fc726",
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "411c7ddfa5c1492ca1f610885725d667",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"<Graph identifier=N304404e3864e4aef8d79731c1ae06af1 (<class 'rdflib.graph.Graph'>)>"
"CytoscapeWidget(cytoscape_layout={'name': 'cola', 'avoidOverlap': True, 'animate': True}, cytoscape_style=[{'s…"
]
},
"execution_count": 9,
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"g.graph.serialize(\"map.ttl\", format='turtle')"
"g.visualise()"
]
},
{
"cell_type": "markdown",
"id": "d18fa37f-ff9f-4b40-8bf0-c8851e0dd145",
"metadata": {},
"source": [
"Add the rest of the structures"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "55e4827c-714f-4caf-ba82-195499bf2fc6",
"metadata": {},
"outputs": [],
"source": [
"g.add_structure_to_graph(struct_Fe)\n",
"g.add_structure_to_graph(struct_Si)"
]
},
{
Expand Down
24 changes: 20 additions & 4 deletions pyscal_rdf/graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,9 @@ def _replace_keys(refdict, indict):
class StructureGraph:
def __init__(self, graph_file=None):
self.graph = Graph()
#owlfile = os.path.join(os.path.dirname(__file__), "data/cmso.owl")
#self.graph.parse(owlfile, format='xml')

self.graph.bind("cmso", CMSO)
if graph_file is not None:
if os.path.exists(graph_file):
Expand Down Expand Up @@ -242,13 +245,21 @@ def add_atoms(self, name=None):



def visualise(self, edge_color="#37474F",
styledict=None, graph_attr ={'rankdir': 'BT'},):
def visualise(self, backend='ipycytoscape',
edge_color="#37474F",
styledict=None,
graph_attr ={'rankdir': 'BT'},
layoutname='cola'):

sdict = defstyledict.copy()
if styledict is not None:
sdict = _replace_keys(sdict, styledict)
return visualize_graph(self.graph, edge_color=edge_color,
styledict=sdict, graph_attr=graph_attr)
return visualize_graph(self.graph,
backend=backend,
edge_color=edge_color,
styledict=sdict,
graph_attr=graph_attr,
layoutname=layoutname)

def write(self, filename, format="json-ld"):
with open(filename, "w") as fout:
Expand Down Expand Up @@ -295,4 +306,9 @@ def to_file(self, sample, filename=None, format="lammps-dump"):
return sys.to_ase()
else:
sys.to_file(filename, format=format)

def serialize(self, filename, format='turtle'):
owlfile = os.path.join(os.path.dirname(__file__), "data/cmso.owl")
self.graph.parse(owlfile, format='xml')


127 changes: 124 additions & 3 deletions pyscal_rdf/visualize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,13 @@
import os
from rdflib import BNode, URIRef, Literal
import uuid
import json
import ipycytoscape

def get_title_from_BNode(x):
return x.toPython()

def get_string_from_URI(x):
def get_string_from_URI(x, ):
raw = x.toPython().split("#")
if len(raw)>1:
return raw[-1]
Expand All @@ -24,10 +26,129 @@ def parse_object(x):
styledict = {
"BNode": {"color": "#ffe6ff", "shape": "box", "style": "filled"},
"URIRef": {"color": "#ffffcc", "shape": "box", "style": "filled"},
"Literal": {"color": "#e6ffcc", "shape": "parallelogram", "style": "filled"},
"Literal": {"color": "#e6ffcc", "shape": "ellipse", "style": "filled"},
}

def visualize_graph(g,
def _switch_box(box):
if box == "box":
return 'rectangle'
#remember that only boxes will be used, circles no!

def _fix_id(string1, istype1):
if istype1 == 'Literal':
id1 = str(uuid.uuid4())
else:
id1 = string1
return id1

def visualize_graph(g,
backend="ipycytoscape",
edge_color="#37474F",
styledict=styledict,
graph_attr ={'rankdir': 'LR'},
layoutname='cola'):
if backend=='ipycytoscape':
return _visualize_graph_ipycytoscape_backend(g,
edge_color=edge_color,
styledict=styledict,
layoutname=layoutname)
else:
return _visualize_graph_graphviz_backend(g,
edge_color=edge_color,
styledict=styledict,
graph_attr=graph_attr)

def _visualize_graph_ipycytoscape_backend(g,
edge_color="#37474F",
styledict=styledict,
layoutname='cola'):
#first step is to create the json file
# we can start with a dict
gdict = {}
gdict["nodes"] = []
gdict["edges"] = []
for k in g:
string1, istype1 = parse_object(k[0])
id1 = _fix_id(string1, istype1)
d = {"data": {"id": str(id1),
"label": str(string1),
"classes": str(istype1),
"shape": _switch_box(styledict[istype1]['shape']),
"width": len(string1)*7,
"fontsize": styledict[istype1]['fontsize']}}
gdict["nodes"].append(d)

string2, istype2 = parse_object(k[2])
id2 = _fix_id(string2, istype2)
d = {"data": {"id": str(id2),
"label": str(string2),
"classes": str(istype2),
"shape": _switch_box(styledict[istype2]['shape']),
"width": len(string2)*7,
"fontsize": styledict[istype1]['fontsize']}}
gdict["nodes"].append(d)

string3, istype3 = parse_object(k[1])
id3 = str(uuid.uuid4())
d = {"data": {"id": str(id3),
"label": str(string3),
"source": id1,
"target": id2,
"fontsize": styledict[istype1]['fontsize']}}
gdict["edges"].append(d)

#graph is complete
#lets try without any customisation
my_style = [
{'selector': 'node',
'style': {
'font-family': 'arial',
'font-size': '10px',
'label': 'data(label)',
'shape': 'data(shape)',
"text-valign": "center",
"text-halign": "center",
"width": 'data(width)',
"font-size": 'data(fontsize)',
}},
{'selector':
'edge',
'style': {
'font-family': 'arial',
'label': 'data(label)',
"font-size": 'data(fontsize)',
"target-arrow-shape": "triangle",
"target-arrow-color": edge_color,
"curve-style": "bezier",
}},
{'selector':
'node[classes="BNode"]',
'style': {
'background-color': styledict['BNode']['color'],
}},
{'selector':
'node[classes="URIRef"]',
'style': {
'background-color': styledict['URIRef']['color'],
}},
{'selector':
'node[classes="Literal"]',
'style': {
'background-color': styledict['Literal']['color']
}},
]

ipycyobj = ipycytoscape.CytoscapeWidget()
ipycyobj.set_layout(
name=layoutname,
avoidOverlap=True,
animate=True,)
ipycyobj.graph.add_graph_from_json(gdict, directed=True)
ipycyobj.set_style(my_style)
return ipycyobj


def _visualize_graph_graphviz_backend(g,
edge_color="#37474F",
styledict=styledict,
graph_attr ={'rankdir': 'LR'},
Expand Down