alpha = minAlpha + t * (maxAlpha - minAlpha)
color = vColor[n]
color[3] = int(alpha)
self.result[n] = color
else:
minValue = inputMetric.getEdgeDoubleMin(self.graph)
maxValue = inputMetric.getEdgeDoubleMax(self.graph)
for e in self.graph.edges():
val = inputMetric[e]
t = getFactor(val - minValue, maxValue - minValue)
alpha = minAlpha + t * (maxAlpha - minAlpha)
color = vColor[e]
color[3] = int(alpha)
self.result[e] = color
return True
pluginDoc = """
Map metric values to alpha component of graph element colors.
In other words, it enables to compute the graph elements transparency
according to the values stored in a numeric property of a graph.
"""
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin('AlphaMapping', 'Alpha Mapping', 'Antoine Lambert',
'20/04/2017', pluginDoc, '1.1')
viewLabel[newClus] = name
viewLabelPosition[newClus] = LabelPositionCluster
viewSize[newClus] = tlp.Size(10,10,10)
viewColor[newClus] = ColorMetanode
TypeNode[newClus] = "Cluster"
IdNeo4j[newClus] = str(remote(NewNeo4jClus)._id)
viewBorderWidth[newClus] = BorderWidthCluster
Nb_Track[newClus] = Nb_Total_Track
image_file = open("temp_image/image_Texture_NewAnnotation" + str(name) + str(Nb_Total_Track) + ".jpg","wb")
image_file.write(texture.decode('base64'))
image_file.close()
path_image = "temp_image/image_Texture_NewAnnotation" + str(name) + str(Nb_Total_Track) + ".jpg"
viewTexture[newClus] = path_image
viewBorderColor[newClus] = ColorBorderUnknow
for node_to_connect in list_node_to_connect:
self.graph.addEdge(node_to_connect,newClus)
parameter_dict = tlp.getDefaultPluginParameters('Fast Overlap Removal')
parameter_dict["x border"] = 5
parameter_dict["y border"] = 5
self.graph.applyLayoutAlgorithm("Fast Overlap Removal", viewLayout,parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jAnnotation", "Adrien", "26/08/2016", "Neo4JCluster", "1.0")
from tulip import *
import tulipplugins
class Test(tlp.Algorithm):
def init(self, context):
tlp.Algorithm.init(self, context)
self.addStringParameter("property", "the property to set", "", True,
True, True)
def check(self):
return (True, "")
def run(self):
return True
tulipplugins.registerPlugin("Test", "A simple Python plugin test", "",
"19/07/2016", "", "1.0")
# set edge colors and border colors to be fully transparent
colors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
borderColors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
# set new border color for nodes
borderColors.setAllNodeValue(borderColor)
# ensure node borders are visible
borderWidths.setAllNodeValue(1.0)
# set the square shape to all leaf nodes
for n in self.graph.getNodes():
if self.graph.outdeg(n) == 0:
shapes[n] = tlp.NodeShape.Square
return True
pluginDoc = '''
Enables to easily configure a treemap layout visualisation for a tree.
As the treemap layout is different from classical node link diagram representation, some
visual properties setup has to be done in order to get an aesthetic visualization of it in Tulip.
This plugin takes care of calling the 'Squarified Tree Map' layout algorithm and adjust
some visual properties to get a correct rendering of the treemap.
'''
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("SquarifiedTreeMapHelper",
"Squarified Tree Map Helper", "Antoine Lambert",
"27/04/2017", pluginDoc, "1.0")
self.graph.applyLayoutAlgorithm('Squarified Tree Map', layout, params)
# set edge colors and border colors to be fully transparent
colors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
borderColors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
# set new border color for nodes
borderColors.setAllNodeValue(borderColor)
# ensure node borders are visible
borderWidths.setAllNodeValue(1.0)
# set the square shape to all leaf nodes
for n in self.graph.getNodes():
if self.graph.outdeg(n) == 0:
shapes[n] = tlp.NodeShape.Square
return True
pluginDoc='''
Enables to easily configure a treemap layout visualisation for a tree.
As the treemap layout is different from classical node link diagram representation, some
visual properties setup has to be done in order to get an aesthetic visualization of it in Tulip.
This plugin takes care of calling the 'Squarified Tree Map' layout algorithm and adjust
some visual properties to get a correct rendering of the treemap.
'''
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("SquarifiedTreeMapHelper", "Squarified Tree Map Helper", "Antoine Lambert", "27/04/2017", pluginDoc, "1.0")
MainviewBorderWidth[NewMetaNode] = MainBorderWidthCluster
image_file = open(
"temp_image/image_Texture_NewCluster" +
str(remote(Newclus)._id) + ".jpg", "wb")
image_file.write(Newtexture.decode('base64'))
image_file.close()
path_image = "temp_image/image_Texture_NewCluster" + str(
remote(Newclus)._id) + ".jpg"
MainviewTexture[NewMetaNode] = path_image
for node_adjacent in list_node_to_connect:
graphMain.addEdge(NewMetaNode, node_adjacent)
parameter_dict = tlp.getDefaultPluginParameters(
'Fast Overlap Removal')
parameter_dict["x border"] = 5
parameter_dict["y border"] = 5
graphMain.applyLayoutAlgorithm("Fast Overlap Removal",
MainviewLayout, parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main",
"Neo4j Extract Tracks And Create New Cluster",
"Adrien", "31/08/2016", "", "1.0")
#print(prop.getNodeStringValue(node))
size = prop.getNodeStringValue(node)[1:-1].split(',')
size = (int(size[0]) + int(size[1])) / 2
os << '"size":%s, ' % size
# node layout
elif prop.getName() == "viewLayout":
coord = prop.getNodeStringValue(node)[1:-1].split(',')
os << '"x":%s, ' % coord[0]
os << '"y":%s, ' % (float(coord[1]) * (-1))
# other
elif prop.getNodeDefaultStringValue() != prop.getNodeStringValue(node) \
and prop.getNodeStringValue(node):
value = prop.getNodeStringValue(node).replace('\\', '\\\\')
value = value.replace('"', '\\\"')
# .replace('"', '\\\"')\
# .replace("\n", "")\
# .replace("\r", "")\
# .replace("\t", "")
os << '"%s":"%s", ' % (prop.getName(), value)
# sigma id
os << '"id":"%s"' % node.id
os << ' }'
os << ']} '
return True
# The line below does the magic to register the plugin to the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("ExportSigma", "SIGMA JSON Export", "Norbert Feron", "01/06/2016",
"Export to sigma.js JSON format", "1.0")
capacity=bipart_g.getDoubleProperty("capacity");
capacity.setAllEdgeValue(0.);
for e in bipart_g.getEdges() :
eo=bipart_g.addEdge(bipart_g.target(e),bipart_g.source(e));
capacity[e]=1.;
## init flow
flow=bipart_g.getDoubleProperty("flow");
flow.setAllEdgeValue(0.);
## compute the maximum matching in the bipartite graph using a maximum flow algorithm
maximumFlow.getMaxFlow(bipart_g,s,t,capacity,flow);
## get the results
bipart_g.delNode(s);
bipart_g.delNode(t);
for e in bipart_g.getEdges() :
if flow[e]>0 :
if e not in map_oends.keys() :
print "Error: unknown edge in maximum matching."
return False;
self.result[map_oends[e]]=True;
# for n in bipart_g.getNodes() :
# self.graph.delNode(n);
# self.graph.delAllSubGraphs(bipart_g);
return True
####################################################################################
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("VertexCycleCover", "Vertex-Disjoint Cycle Cover", "Francois Queyroi", "30/11/2017", "Find a Vertex-Disjoint Cycle Cover", "1.0")
## if the assignment is not secret (due to e1) we remove e1 and look for a new assignment
if not keep_e1:
result_found = False
G.delEdge(e1)
break
## get the results
if not self.oriented:
for e in self.graph.getEdges():
if not copy.isElement(e):
if self.result[e]:
s, t = self.graph.ends(e)
oe = self.graph.existEdge(t, s, True)
self.result[oe] = True
self.graph.delEdge(e)
self.graph.delAllSubGraphs(G)
self.graph.delAllSubGraphs(copy)
if not result_found:
self.pluginProgress.setError("Graph " + self.graph.getName() +
" has no Secret Santa Assignment !")
self.result.setAllEdgeValue(False)
return result_found
####################################################################################
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("SecretSanta", "Secret Santa", "Francois Queyroi",
"30/11/2017", "Find a Secret Santa Assignment",
"1.0")
idTrack = IdNeo4j[NodeTlp]
viewBorderColor[NodeTlp] = ColorBorderValide
statement = 'MATCH (clus) '\
'WHERE ID(clus)=' + str(idMeta) + \
' MATCH (track) '\
'WHERE ID(track)=' + str(idTrack) + \
' MATCH (clus)-[r:CLUSTERED]->(track) '\
'SET r.isValidated = "Valide"'
graphNeo4j.run(statement)
else:
#Sinon c'est qu'on est sur le graph Main. Seul les cluster peuvent etre valides
for NodeTlp in viewSelection.getNodesEqualTo(True):
if TypeNode[NodeTlp] == "Cluster":
idCluster = IdNeo4j[NodeTlp]
viewBorderColor[NodeTlp] = ColorBorderValide
statement = 'MATCH (algo:Algo {name:"' + 'user_defined' + '"}) '\
' MATCH (clus) '\
'WHERE ID(clus)=' + str(idCluster) + \
' OPTIONAL MATCH (clus)-[r:INVALIDATED_BY]->(algo) '\
'DELETE r '\
'MERGE (clus)-[:VALIDATED_BY]->(algo)'
graphNeo4j.run(statement)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jValidate", "Adrien", "29/08/2016",
"Neo4JCluster", "1.0")
from tulip import *
from SqlReader import *
from GraphView import *
import tulipplugins
import ntpath
class SQLImport(tlp.ImportModule):
def __init__(self, context):
tlp.ImportModule.__init__(self, context)
self.addStringParameter("file::SQL script", "Script SQL you want to add in a graph")
# You can add parameters to the plugin here through the following syntax:
# self.add<Type>Parameter("<paramName>", "<paramDoc>", "<paramDefaultValue>")
# (see the documentation of class tlp.WithParameter to see what parameter types are supported).
def importGraph(self):
filename = self.dataSet["file::SQL script"];
name = ntpath.basename(filename)
self.graph.setName(name)
sql_reader = SqlReader(filename, self.graph)
sql_reader.compute_diagram()
g = GraphView(self.graph)
g.set_view()
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("SQLImport", "Import SQL", "", "12/06/2017", "", "1.0")
# Loop over all edges. If edge is a gap junction, then search for a gap junction going the other direction.
for edge in graph.getEdges():
edgeType = tp.utils.getEdgeType(edge, graph)
if edgeType == self.dataSet[self._edgeTypeLabel]:
source = graph.source(edge)
target = graph.target(edge)
links = linkedStructures[edge]
if not self.findInverseEdge(graph, source, target, links):
output = str(tp.utils.getNodeId(
source, graph)) + "-" + tp.utils.getNodeType(
source, graph) + "; " + str(
tp.utils.getNodeId(
target,
graph)) + "-" + tp.utils.getNodeType(
target, graph) + "; " + links
viewSelection[edge] = True
self.printToFile(output)
self.endFileOutput()
return True
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("BidirectionalSynapseCleanup",
"Find Missing Bidirectional Synapses", "Kerzner",
"12/01/2017", "", "1.0")
from FindPathsPlugin import FindPathsPlugin
import tulipplugins
class FindPaths0(FindPathsPlugin):
""" Tulip plugin algorithm which searches for 1-hop paths """
def __init__(self, context):
FindPathsPlugin.__init__(self, context, 0)
# The line below does the magic to register the plugin to the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("FindPaths0", "Find Nodes (Regex)", "Nathaniel Nelson", "9/3/2016", "", "1.0")
from FindPathsPlugin import FindPathsPlugin
import tulipplugins
class FindPaths0(FindPathsPlugin):
""" Tulip plugin algorithm which searches for 1-hop paths """
def __init__(self, context):
FindPathsPlugin.__init__(self, context, 0)
# The line below does the magic to register the plugin to the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("FindPaths0", "Find Nodes (Regex)",
"Nathaniel Nelson", "9/3/2016", "", "1.0")
day = int(dict(record[0][2])["name"])
month = int(dict(record[0][3])["name"])
year = int(dict(record[0][4])["name"])
num_track = int(dict(record[0][1])["num_track"])
num_shot = int(dict(record[0][1])["num_shot"])
#infos = year + "_" + month + "_" + day + "_" + num_shot + "_" + num_track
infos = "%04d_%02d_%02d_19_00-shot%02d_%d-Track%d"%(year,month,day,day,num_shot,num_track)
dict_cluster[infos] = "Cluster " + str(num_clus)
namefile = ""
for d in dateStart:
namefile += d + "_"
namefile += "to_"
for d in dateEnd:
namefile += d + "_"
namefile = namefile[0:-1]
with open('Resultat_cluster/' + namefile + '.json', 'w') as f:
json.dump(dict_cluster, f, indent=4,sort_keys=True)
f.close()
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "neo4j Clusters to file", "Adrien", "07/09/2016", "", "1.0")
continue;
for num in xrange(2, len(fieldnames)):
patient = fieldnames[num]
if row[patient] == '':
continue
if not patient in addedNodes:
addedNodes[patient] = self.create_node(node, patient, createParams)
createParams['coords'] -= tlp.Vec3f(10,0,0)
edge = self.graph.addEdge(addedNodes[patient], node, {self.EDGE_TYPE_COL:row[patient], "viewColor":createParams['edgesColor']})
self.pluginProgress.progress(i, rlen)
if self.pluginProgress.state() == tlp.TLP_CANCEL:
self.graph.delNodes(addedNodes.values(), True)
return 0;
def getUserColor(self, param):
try:
c = self.dataSet[param]
color = tlp.Color(c.getR(),c.getG(),c.getB(),c.getA())
return color
except Exception:
return tlp.Color(0,0,0,255);
def printerr(self, message):
self.pluginProgress.setError(message)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("MergeSamples", "VisuDNA - Merge Samples", "SB", "27/11/2017", "", "1.0")
for e in main_sub.getEdges():
viewSize[e] = e2size[e]
n2size = {n: viewSize[n] for n in main_sub.getNodes()}
parameter_dict = tlp.getDefaultPluginParameters('Size Mapping')
parameter_dict["result"] = viewSize
parameter_dict["input"] = viewSize
parameter_dict["property"] = Nb_Track
parameter_dict["node/edge"] = False
parameter_dict["min size"] = 0.2
parameter_dict["max size"] = 3.0
parameter_dict["area proportional"] = "Area Proportional"
main_sub.applySizeAlgorithm("Size Mapping", viewSize, parameter_dict)
for n in main_sub.getNodes():
viewSize[n] = n2size[n]
parameter_dict = tlp.getDefaultPluginParameters('Fast Overlap Removal')
parameter_dict["x border"] = 5
parameter_dict["y border"] = 5
main_sub.applyLayoutAlgorithm("Fast Overlap Removal", viewLayout,
parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jConnect", "Adrien", "16/08/2016",
"Neo4JCluster", "1.0")
num_shot) + "_" + str(num_track) + ".jpg"
viewTexture[node_track] = path_image
viewLayout[node_track] = tlp.Coord(
ReferencePositionX + float(SizePicture / 2.0),
ReferencePositionY + float(SizePicture / 2.0), 0)
node_date = Rootgraph.addNode()
subgraph.addNode(node_date)
viewSize[node_date] = SizeYear
viewShape[node_date] = ShapeYear
viewColor[node_date] = ColorYear
viewLabel[node_date] = year
viewLayout[node_date] = tlp.Coord(
(ReferencePositionX + SizePicture +
ReferencePositionDebutYearX) / 2.0 + 30.0,
ReferencePositionDebutYearY - 80, 0)
ReferencePositionX = 0.0
ReferencePositionY = ReferencePositionDebutYearY + float(
MaxHauteur) * (float(SizePicture) +
float(SizeInterPicture)) + 115.0
AirtimeMeta[Metanode] = airtime
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jLoadHistogramme", "Adrien",
"24/08/2016", "Neo4JCluster", "1.0")
from FindPathsPlugin import FindPathsPlugin
import tulipplugins
class FindPaths1(FindPathsPlugin):
""" Tulip plugin algorithm which searches for 1-hop paths """
def __init__(self, context):
FindPathsPlugin.__init__(self, context, 1)
# The line below does the magic to register the plugin to the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("FindPaths1", "Find 1-Hop Paths (Regex)",
"Nathaniel Nelson", "9/3/2016", "", "1.0")
alpha = minAlpha + t * (maxAlpha - minAlpha)
color = self.result[n]
color[3] = int(alpha)
self.result[n] = color
else:
minValue = inputMetric.getEdgeDoubleMin(self.graph)
maxValue = inputMetric.getEdgeDoubleMax(self.graph)
for e in self.graph.getEdges():
val = inputMetric[e]
t = getFactor(val - minValue, maxValue - minValue)
alpha = minAlpha + t * (maxAlpha - minAlpha)
color = self.result[e]
color[3] = int(alpha)
self.result[e] = color
return True
pluginDoc = '''
Map metric values to alpha component of graph element colors.
In other words, it enables to compute the graph elements transparency according to the values
stored in a numeric property of a graph.
'''
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("AlphaMapping", "Alpha Mapping", "Antoine Lambert",
"20/04/2017", pluginDoc, "1.0")
label = str(record.type())
print label
if label == "VALIDATED_BY":
viewBorderColor[NewNode] = ColorBorderValide
elif label == "INVALIDATED_BY":
viewBorderColor[NewNode] = ColorBorderInvalide
viewBorderColor[NewNode] = ColorBorderUnknow
viewSize[NewNode] = tlp.Size(10, 10, 10)
viewColor[NewNode] = ColorCluster
if str(nameClus) != "":
viewLabel[NewNode] = str(nameClus)
viewLabelPosition[NewNode] = LabelPositionMetanode
viewShape[NewNode] = ShapeMetanodeAnnote
else:
viewShape[NewNode] = ShapeMetanodeNotAnnote
parameter_dict = tlp.getDefaultPluginParameters('Fast Overlap Removal')
parameter_dict["x border"] = 5
parameter_dict["y border"] = 5
self.graph.applyLayoutAlgorithm("Fast Overlap Removal", viewLayout,
parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jMerge", "Adrien", "26/08/2016",
"Neo4JCluster", "1.0")
from tulip import tlp
import tulipplugins
class Test(tlp.Algorithm):
def init(self, context):
tlp.Algorithm.init(self, context)
self.addStringParameter("property", "the property to set", "", True, True, True)
def check(self):
return (True, "")
def run(self):
return True
tulipplugins.registerPlugin("Test", "A simple Python plugin test", "", "19/07/2016", "", "1.0")
self.simple = True
self.icon.configure(image=self.simple_link_icon)
self.type_frame.grid()
self.min_frame.grid_remove()
self.middle_frame.grid_remove()
self.max_frame.grid_remove()
update_global_query()
def update_max(self):
"""Update max spinner value if min value is greater"""
if self.max.get() < self.min.get():
self.max.set(self.min.get())
def update_min(self):
"""Update min spinner value if max value is lower"""
if self.max.get() < self.min.get():
self.min.set(self.max.get())
init = Node()
init.update_name_list()
update_global_query()
work_frame.on_frame_configure()
root.mainloop()
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("NeOmics", "Query Maker", "Eliot Ragueneau et Jean Clément Gallardo", "11/05/2019",
"Help to build a cypher query describing a neo4j graph that will be drawn on Tulip", "1.0")
year) + "_" + str(month) + "_" + str(
day) + "_" + str(num_shot) + "_" + str(
num_track) + ".jpg"
viewTexture[track_node] = path_image
parameter_dict = tlp.getDefaultPluginParameters('FM^3 (OGDF)')
parameter_dict["Unit edge length"] = 3
subgraphAlgoLayout.applyLayoutAlgorithm(
"FM^3 (OGDF)", viewLayout, parameter_dict)
Correction = viewLayout[NodeTlp] - initialLayout
for node_to_modify in subgraphAlgoLayout.getNodes():
viewLayoutMain[node_to_modify] = tlp.Coord(
viewLayout[node_to_modify][0] - Correction[0],
viewLayout[node_to_modify][1] - Correction[1],
viewLayout[node_to_modify][2] - Correction[2])
print viewLayout[NodeTlp]
self.graph.delSubGraph(subgraphAlgoLayout)
parameter_dict = tlp.getDefaultPluginParameters('Fast Overlap Removal')
parameter_dict["x border"] = 1
parameter_dict["y border"] = 1
self.graph.applyLayoutAlgorithm("Fast Overlap Removal", viewLayout,
parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4j Explore Date", "Adrien",
"02/09/2016", "", "1.0")
idTrack = IdNeo4j[NodeTlp]
viewBorderColor[NodeTlp] = ColorBorderInvalide
statement = 'MATCH (clus) '\
'WHERE ID(clus)=' + str(idMeta) + \
' MATCH (track) '\
'WHERE ID(track)=' + str(idTrack) + \
' MATCH (clus)-[r:CLUSTERED]->(track) '\
'SET r.isValidated = "NotValide"'
graphNeo4j.run(statement)
else:
#Sinon c'est qu'on est sur le graph Main. Seul les cluster peuvent etre valides
for NodeTlp in viewSelection.getNodesEqualTo(True):
if TypeNode[NodeTlp] == "Cluster":
idCluster = IdNeo4j[NodeTlp]
viewBorderColor[NodeTlp] = ColorBorderInvalide
statement = 'MATCH (algo:Algo {name:"' + 'user_defined' + '"}) '\
' MATCH (clus) '\
'WHERE ID(clus)=' + str(idCluster) + \
' OPTIONAL MATCH (clus)-[r:VALIDATED_BY]->(algo) '\
'DELETE r '\
'MERGE (clus)-[:INVALIDATED_BY]->(algo)'
print statement
graphNeo4j.run(statement)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jInvalidate", "Adrien", "29/08/2016",
"", "1.0")
fm3Properties = tlp.getDefaultPluginParameters('FM^3 (OGDF)', graph=None)
fm3Properties['Edge Length Property'] = self.distance
self.graph.applyLayoutAlgorithm('FM^3 (OGDF)', self.viewLayout, fm3Properties)
def colorLoci(self):
self.colorLociByExpression('intergenic', tlp.Color(222, 212, 195, 80))
self.colorLociByExpression('up', tlp.Color(0, 255, 0))
self.colorLociByExpression('down', tlp.Color(255, 0, 0))
self.colorLociByExpression('stable', tlp.Color(0, 0, 0, 80))
self.colorLociByExpression('', tlp.Color(0, 0, 0, 80))
self.colorLociByExpression('nan', tlp.Color(255, 230, 255, 80))
def colorLociByExpression(self, expression, color):
for loci in self.expression.getNodesEqualTo(expression):
self.viewColor[loci] = color
def colorInteractions(self):
self.colorInteractionsByStatus('gain', tlp.Color(0, 255, 0))
self.colorInteractionsByStatus('stable', tlp.Color(0, 0, 0, 80))
self.colorInteractionsByStatus('loss', tlp.Color(255, 0, 0))
def colorInteractionsByStatus(self, interactionStatus, color):
for interaction in self.interactionStatus.getEdgesEqualTo(interactionStatus):
self.viewColor[interaction] = color
def setLociSize(self):
self.viewSize.setAllNodeValue(tlp.Vec3f(1e5, 1e5, 0.5))
tulipplugins.registerPlugin("InteractionNetwork", "Interaction Network", "AM2E", "28/01/2020", "", "1.0")
statement = 'MATCH (user_defined:User_Defined_Cluster) '\
'MATCH (user_defined)-[r]-() '\
'DELETE r '
tx.run(statement)
statement = 'MATCH (user_defined:User_Defined_Cluster) '\
'DELETE user_defined'
tx.run(statement)
statement = 'MATCH ()-[r:CLUSTERED]->() '\
'SET r.isValidated = "Unknow" '
tx.run(statement)
statement = 'MATCH (n) '\
'WHERE size(labels(n)) = 0 '\
'DELETE n'
tx.run(statement)
tx.commit()
neo4j_commit.correct_name(graphNeo4j)
neo4j_commit.merge_overlap_cluster(graphNeo4j)
neo4j_commit.load_all_texture(graphNeo4j)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jClearAllModification", "Adrien",
"29/08/2016", "", "1.0")
from FindPathsPlugin import FindPathsPlugin
import tulipplugins
class FindPaths1(FindPathsPlugin):
""" Tulip plugin algorithm which searches for 1-hop paths """
def __init__(self, context):
FindPathsPlugin.__init__(self, context, 1)
# The line below does the magic to register the plugin to the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("FindPaths1", "Find 1-Hop Paths (Regex)", "Nathaniel Nelson", "9/3/2016", "", "1.0")
delta.setAllNodeValue(0.)
ancestors, stack, nb_paths = self.shortestPaths(src, chossen_iterator)
while len(stack) > 0:
w = stack.pop()
flow_sw = self.flow_amount(src, w)/2.
# flow divided by two since flows are undirected
total_flow += flow_sw
if w != src :
self.result[w] += delta[w]
for v in ancestors[w] :
inc_delta = (nb_paths[v]/nb_paths[w])*(flow_sw + delta[w])
delta[v] += inc_delta
e = self.graph.existEdge(v, w, False)
if self.dataSet["type"] == "Out":
e = self.graph.existEdge(v, w, True)
if self.dataSet["type"] == "In":
e = self.graph.existEdge(w, v, True)
self.result[e] += inc_delta
val = 1.
if self.cost is not None:
val = self.cost[e]
avg_path_length += val * inc_delta
self.dataSet["average path length"] = avg_path_length
self.dataSet["total flow"] = total_flow
return True
#########################################################################################################
tulipplugins.registerPlugin("BetweennessGravityModel", "Betweenness Gravity Model", "Francois Queyroi", "02/04/2019", "", "1.0")
colors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
borderColors.setAllEdgeValue(tlp.Color(0, 0, 0, 0))
# set new border color for nodes
borderColors.setAllNodeValue(borderColor)
# ensure node borders are visible
borderWidths.setAllNodeValue(1.0)
# set the square shape to all leaf nodes
for n in self.graph.getNodes():
if self.graph.outdeg(n) == 0:
shapes[n] = tlp.NodeShape.Square
return True
pluginDoc = """
Enables to easily configure a treemap layout visualisation for a tree.
As the treemap layout is different from classical node link diagram
representation, some visual properties setup has to be done in order
to get an aesthetic visualization of it in Tulip.
This plugin takes care of calling the 'Squarified Tree Map' layout algorithm
and adjust some visual properties to get a correct rendering of the treemap.
"""
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin('SquarifiedTreeMapHelper',
'Squarified Tree Map Helper', 'Antoine Lambert',
'27/04/2017', pluginDoc, '1.0')
val = inputMetric[n]
t = getFactor(val - minValue, maxValue - minValue)
alpha = minAlpha + t * (maxAlpha - minAlpha)
color = vColor[n]
color[3] = int(alpha)
self.result[n] = color
else:
minValue = inputMetric.getEdgeDoubleMin(self.graph)
maxValue = inputMetric.getEdgeDoubleMax(self.graph)
for e in self.graph.edges():
val = inputMetric[e]
t = getFactor(val - minValue, maxValue - minValue)
alpha = minAlpha + t * (maxAlpha - minAlpha)
color = vColor[e]
color[3] = int(alpha)
self.result[e] = color
return True
pluginDoc = '''
Map metric values to alpha component of graph element colors.
In other words, it enables to compute the graph elements transparency according to the values
stored in a numeric property of a graph.
'''
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("AlphaMapping", "Alpha Mapping", "Antoine Lambert", "20/04/2017", pluginDoc, "1.1")
'MATCH (label)-[allRel]-() '\
'DELETE r '
if nb_rel == 1:
statement += 'DELETE allRel '\
'DELETE label'
graphNeo4j.run(statement)
statement = 'MATCH (clus) '\
'WHERE ID(clus)='+ str(remote(clusNeo4j)._id) + \
' MATCH (clus)-[r]-() '\
'DELETE r '\
'DELETE clus'
graphNeo4j.run(statement)
#We suprress the MetaCluster if there is no track left
graphRoot.delNode(MetaCluster)
parameter_dict = tlp.getDefaultPluginParameters(
'Fast Overlap Removal')
parameter_dict["x border"] = 5
parameter_dict["y border"] = 5
graphMain.applyLayoutAlgorithm("Fast Overlap Removal",
MainviewLayout, parameter_dict)
return True
# The line below does the magic to register the plugin into the plugin database
# and updates the GUI to make it accessible through the menus.
tulipplugins.registerPlugin("Main", "Neo4jRemoveFromCluster", "Adrien",
"29/08/2016", "", "1.0")
