def g2pair(self,ni,nf,ei,ef1,ef2,ew,numFile,mapFile,weightFile):
inobj = []
inobj.append(nm.mcut(f="%s:node"%(ef1),i=ei ).msetstr(a="flag",v=0))
inobj.append(nm.mcut(f="%s:node"%(ef2),i=ei ).msetstr(a="flag",v=0))
if nf :
inobj.append(nm.mcut(f="%s:node"%(nf),i=ni ).msetstr(a="flag",v=1))
f = nm.mbest(i=inobj,k="node",s="flag",fr=0,size=1 )
# isolated nodes are set to the end of position in mapping file.
# S= must start from 0 (but inside R vertex number will be added one)
f <<= nm.mnumber(s="flag,node",a="num",S=0,o=mapFile)
f.run()
f = None
f <<= nm.mcut(f=[ef1,ef2] , i=ei)
f <<= nm.mjoin( k=ef1 , K="node" , m=mapFile ,f="num:num1")
f <<= nm.mjoin( k=ef2 , K="node" , m=mapFile ,f="num:num2")
f <<= nm.mcut(f="num1,num2")
f <<= nm.mfsort(f="num1,num2")
f <<= nm.msortf(f="num1%n,num2%n",nfno=True)
f <<= nm.cmd("tr ',' ' ' " )
f <<= nm.mwrite(o=numFile)
f.run()
nodeSize=mrecount(i=mapFile)
if ew:
nm.mcut(f=ew,i=ei,o=weightFile).run()
else:
ew="weight"
nm.msetstr(v=1,a=ew,i=ei).mcut(f=ew,o=weightFile).run()
return nodeSize
def g2pair(self,ni,nf,ei,ef1,ef2,ew,numFile,mapFile,weightFile):
#MCMD::msgLog("converting graph files into a pair of numbered nodes ...")
#wf=MCMD::Mtemp.new
#wf1=wf.file
#wf2=wf.file
#wf3=wf.file
allinObj =[]
wf1 = nm.mcut(f="%s:node"%(ef1),i=ei ).msetstr(v=0,a="flag")
wf2 = nm.mcut(f="%s:node"%(ef2),i=ei ).msetstr(v=0,a="flag")
f = None
if nf:
f <<= nm.mcut(i=[wf1,wf2,nm.mcut(f=nf+":node",i=ni).msetstr(v=1,a="flag")],f="node,flag")
f <<= nm.mbest(k="node" , s="flag" , fr=0 ,size=1)
else:
f <<= nm.mcut(i=[wf1,wf2],f="node,flag")
f <<= nm.muniq(k="node")
f <<= nm.mnumber(s="flag,node",a="num",S=0,o=mapFile)
f.run()
f = None
f <<= nm.mcut(f=[ef1,ef2],i=ei)
f <<= nm.mjoin(k=ef1 , K="node",m=mapFile , f="num:num1")
f <<= nm.mjoin(k=ef2 , K="node",m=mapFile , f="num:num2")
f <<= nm.mcut(f="num1,num2")
f <<= nm.mfsort(f="num1,num2")
f <<= nm.msortf(f="num1%n,num2%n",nfno=True)
f <<= nm.cmd("tr ',' ' ' ")
f <<= nm.mwrite(o=numFile)
f.run()
if ew :
nm.mcut(f=ew,i=ei,o=weightFile).run()
else:
ew="weight"
nm.msetstr(v=1 , a=ew ,i=ei).mcut(f=ew,o=weightFile).run()
nodeSize=mrecount(i=mapFile)
return nodeSize
def g2pair(self, ni, nf, ei, ef1, ef2, numFile, mapFile):
#MCMD::msgLog("converting graph files into a pair of numbered nodes ...")
#wf=MCMD::Mtemp.new
#wf1=wf.file
#wf2=wf.file
#wf3=wf.file
inobj = []
inobj.append(nm.mcut(f="%s:node" % (ef1), i=ei).msetstr(a="flag", v=0))
inobj.append(nm.mcut(f="%s:node" % (ef2), i=ei).msetstr(a="flag", v=0))
if nf:
inobj.append(
nm.mcut(f="%s:node" % (nf), i=ni).msetstr(a="flag", v=1))
f = nm.mbest(i=inobj, k="node", s="flag", fr=0, size=1)
# isolated nodes are set to the end of position in mapping file.
# S= must start from 0 (but inside R vertex number will be added one)
f <<= nm.mnumber(s="flag,node", a="num", S=0, o=mapFile)
f.run()
f = None
f <<= nm.mcut(f=[ef1, ef2], i=ei)
f <<= nm.mjoin(k=ef1, K="node", m=mapFile, f="num:num1")
f <<= nm.mjoin(k=ef2, K="node", m=mapFile, f="num:num2")
f <<= nm.mcut(f="num1,num2")
#f << "mfsort f=num1,num2 |"
f <<= nm.msortf(f="num1%n,num2%n", nfno=True)
f <<= nm.cmd("tr ',' ' ' ")
f <<= nm.mwrite(o=numFile)
f.run()
nodeSize = mrecount(i=mapFile)
return nodeSize
def run(self):
temp = mtemp.Mtemp()
### mtra2gc
xxsimgN = temp.file()
xxsimgE = temp.file()
xxsimgE0 = temp.file()
param = {}
param["i"] = self.iFile
if self.idFN:
param["tid"] = self.idFN
if self.itemFN:
param["item"] = self.itemFN
if self.sp1:
param["s"] = self.sp1
if self.sp2:
param["S"] = self.sp2
#####################
# 異なる向きのconfidenceを列挙するためにsim=C th=0として双方向列挙しておく
# 出力データは倍になるが、mfriendsで-directedとすることで元が取れている
param["sim"] = "C"
param["th"] = "0"
param["node_support"] = True
if self.numtp:
param["num"] = True
param["no"] = xxsimgN
param["eo"] = xxsimgE0
nt.mtra2gc(**param).run()
f = nm.readcsv(xxsimgE0)
for i in range(self.filterSize):
f <<= nm.mselnum(f=self.filter[i],
c="[%s,%s]" % (self.lb[i], self.ub[i]))
f <<= nm.writecsv(xxsimgE)
f.run()
### mfrirends
xxfriends = temp.file()
xxfriendE = temp.file()
xxw = temp.file()
xxf = temp.file()
xxff = temp.file()
xxor = temp.file()
if not os.path.isdir(xxfriends):
os.makedirs(xxfriends)
col = [["FF000080", "FF888880"], ["0000FF80", "8888FF80"],
["00FF0080", "88FF8880"]]
for i in range(len(self.sim)):
paramf = {}
paramf["ei"] = xxsimgE
paramf["ni"] = xxsimgN
paramf["ef"] = "node1,node2"
paramf["nf"] = "node"
paramf["eo"] = xxfriendE
paramf["no"] = xxfriends + "/n_" + str(i)
paramf["sim"] = self.sim[i]
paramf["dir"] = self.dir[i]
paramf["rank"] = self.rank[i]
paramf["directed"] = True
nt.mfriends(**paramf).run()
frec2 = nm.mfsort(f="node1,node2", i=xxfriendE)
frec2 <<= nm.msummary(k="node1,node2",
f=self.sim[i],
c="count,mean")
frec2 <<= nm.mselstr(f="count", v=2)
# node1%0,node2%1,fld,count,mean
# a,b,support,2,0.1818181818
# a,d,support,2,0.1818181818
f = nm.mjoin(k="node1,node2",
K="node1,node2",
m=frec2,
f="mean:s1",
n=True,
i=xxfriendE)
f <<= nm.mjoin(k="node2,node1",
K="node1,node2",
m=frec2,
f="mean:s2",
n=True)
# 1) xxrecs2でsimをjoinできない(s1,s2共にnull)ということは、それは片方向枝なので"F"をつける
# 2) 双方向枝a->b,b->aのうちa->bのみ(s1がnullでない)に"W"の印をつける。
# 3) それ以外の枝は"D"として削除
f <<= nm.mcal(
c='if(isnull($s{s1}),if(isnull($s{s2}),\"F\",\"D\"),\"W\")',
a="dir")
f <<= nm.mselstr(f="dir", v="D", r=True)
f <<= nm.mcal(c='if($s{dir}==\"W\",$s{s1},$s{%s})' % (self.sim[i]),
a="sim")
f <<= nm.mchgstr(f="dir:color",
c='W:%s,F:%s' % (col[i][0], col[i][1]),
A=True)
f <<= nm.msetstr(v=[self.sim[i], str(i)], a="simType,simPriority")
f <<= nm.mcut(f="simType,simPriority,node1,node2,sim,dir,color",
o=xxfriends + "/e_" + str(i))
f.run()
# node1%1,node2%0,simType,sim,dir,color
# b,a,jaccard,0.3333333333,F,8888FF
# j,c,jaccard,0.3333333333,F,8888FF
# b,d,jaccard,0.3333333333,F,8888FF
# a,e,jaccard,0.5,W,0000FF
# d,e,jaccard,0.5,W,0000FF
# rule fileの出力
if self.orFile:
mmm = nm.mcat(i=xxfriends + "/e_*").muniq(k="node1,node2")
nm.mcommon(k="node1,node2", i=xxsimgE, m=mmm, o=self.orFile).run()
# マルチ枝の単一化(W優先,パラメータ位置優先)
if self.prune:
"""
# 双方向と片方向に分割
nm.mcat(i=xxfriends+"/e_*").mselstr(f="dir",v="W",o=xxw,u=xxf).run()
# 片方向のみの枝を選択
f = nm.mcommon(k="node1,node2",K="node1,node2",r=True,m=xxw,i=xxf)
f <<= nm.mcommon(k="node1,node2",K="node2,node1",r=True,m=xxw,o=xxff)
f.run()
f = nm.mcat(i=xxw+","+xxff).mbest(k="node1,node2",s="dir%r,simPriority%n",o=self.oeFile).run()
"""
#これだめ
fo = nm.mcat(i=xxfriends + "/e_*").mselstr(f="dir", v="W")
fu = fo.direction("u") # これは再考
fu <<= nm.mcommon(k="node1,node2", K="node1,node2", r=True, m=fo)
fu <<= nm.mcommon(k="node1,node2", K="node2,node1", r=True, m=fo)
#f = nm.m2cat()
f = nm.mbest(i=[fo, fu],
k="node1,node2",
s="dir%r,simPriority%n",
o=self.oeFile)
f.run()
else:
nm.mcat(i=xxfriends + "/e_*", o=self.oeFile).run()
nm.mcat(i=xxfriends + "/n_0", o=self.onFile).run()
def mnetpie(ei,
ni,
ef,
nf,
o,
nodeSizeFld=None,
nodeTipsFld=None,
nodeColorFld=None,
edgeWidthFld=None,
edgeColorFld=None,
pieDataFld=None,
pieTipsFld=None,
picFld=None,
undirect=False,
offline=False):
#ei:edge file
#ef:egfile
if type(ef) is str:
ef = ef.split(',')
if len(ef) != 2:
raise Exception("ef= takes just two field names")
if not ((pieDataFld == None and pieTipsFld == None) or
(pieDataFld != None and pieTipsFld != None)):
raise Exception(
"pieDataFld= pieTipsFld= are necessary at the same time")
if picFld != None and pieDataFld != None:
raise Exception(
"picFld= cannot be specified with pieDataFld= pieTipsFld=")
if nodeColorFld != None:
if picFld != None or pieDataFld != None or pieTipsFld != None:
raise Exception(
"nodeColorFld= cannot be specified with pieDataFld= pieTipsFld= picFld="
)
if pieDataFld != None and pieTipsFld != None:
caseNo = 1
elif picFld != None:
caseNo = 2
else:
caseNo = 0
tempW = mtemp.Mtemp()
xxnode = tempW.file()
nodefld = []
nodedmy1 = []
nodedmy2 = []
nodefld.append("%s:node" % (nf))
if nodeSizeFld != None:
nodefld.append("%s:nodesize" % (nodeSizeFld))
else:
nodedmy1.append("nodesize")
nodedmy2.append("50")
if nodeTipsFld != None:
nodefld.append("%s:nodeT" % (nodeTipFld))
else:
nodedmy1.append("nodeT")
nodedmy2.append("")
if nodeColorFld != None:
nodefld.append("%s:nodeClr" % (nodeColorFld))
else:
nodedmy1.append("nodeClr")
nodedmy2.append("skyblue")
if caseNo == 1:
nodefld.append("%s:pieD" % (pieDataFld))
nodefld.append("%s:pieT" % (pieTipsFld))
elif caseNo == 2:
nodefld.append("%s:pic" % (picFld))
else:
nodedmy1.append("pic")
nodedmy2.append("")
f1 = None
f1 <<= nm.mcut(i=ni, f=nodefld)
if len(nodedmy1) != 0:
f1 <<= nm.msetstr(a=nodedmy1, v=nodedmy2)
if caseNo == 1:
f1 <<= nm.mshare(k="node", f="pieD:pieDS")
f1 <<= nm.mnumber(k="node", a="nodeid", B=True)
f2 = nm.muniq(k="pieT", i=f1)
f2 <<= nm.mnumber(q=True, a="pieTno")
f2 <<= nm.mjoin(k="pieT", f="pieTno", i=f1).iredirect("m")
f2 <<= nm.msortf(f="nodeid%n,pieTno%n", o=xxnode)
else:
f2 = nm.mnumber(a="nodeid%n", q=True, i=f1, o=xxnode)
f2.run()
xxedge = tempW.file()
# MAKE EDGE DATA
edgefld = []
edgedmy1 = []
edgedmy2 = []
edgefld.append("%s:edgeS" % (ef[0]))
edgefld.append("%s:edgeE" % (ef[1]))
if edgeWidthFld != None:
edgefld.append("%s:edgesize" % (edgeWidthFld))
else:
edgedmy1.append("edgesize")
edgedmy2.append("1")
if edgeColorFld != None:
edgefld.append("%s:edgecolor" % (edgeColorFld))
else:
edgedmy1.append("edgecolor")
edgedmy2.append("black")
f3 = None
f3 <<= nm.mcut(i=ei, f=edgefld)
if len(edgedmy1) != 0:
f3 <<= nm.msetstr(a=edgedmy1, v=edgedmy2)
f3 <<= nm.mnumber(a="preNo", q=True)
f3 <<= nm.mbest(k="edgeS,edgeE", s="preNo%nr")
f3 <<= nm.mnumber(s="preNo%n", a="edgeID")
f3 <<= nm.mjoin(k="edgeS", K="node", f="nodeid:edgeSid", m=xxnode)
f3 <<= nm.mjoin(k="edgeE", K="node", f="nodeid:edgeEid", m=xxnode)
#双方向チェック一応
f4 = None
f4 <<= nm.mfsort(i=f3, f="edgeS,edgeE")
f4 <<= nm.mcount(k="edgeS,edgeE", a="edgecnt")
f4 <<= nm.mselnum(c="[2,]", f="edgecnt")
f4 <<= nm.msetstr(a="biflg", v=1)
f4 <<= nm.mjoin(k="edgeID", f="biflg", n=True, i=f3).iredirect("m")
f4 <<= nm.msortf(f="edgeID%n", o=xxedge)
f4.run()
gdata = "{\"nodes\":["
if caseNo == 1:
nodedatastk = []
nodedatas = ""
for val, top, bot in nm.readcsv(xxnode).getline(k="nodeid",
otype='dict',
q=True):
name = val["node"]
r = val["nodesize"]
title = val["nodeT"]
if top:
nodedatas = "{\"name\":\"%s\",\"title\":\"%s\",\"r\":%s,\"node\":[" % (
name, title, r)
pieTno = val["pieTno"]
pieT = val["pieT"]
pieDS = val["pieDS"]
nodedatas += "{\"group\":%s,\"color\":%s,\"value\":%s,\"title\":\"%s\"}" % (
pieTno, pieDS, pieDS, pieT)
if bot:
nodedatas += "]}"
nodedatastk.append(nodedatas)
nodedatas = ""
else:
nodedatas += ","
gdata += ",".join(nodedatastk)
else:
nodedatastk = []
for val in nm.readcsv(xxnode).getline(otype='dict'):
name = val["node"]
r = val["nodesize"]
title = val["nodeT"]
pic = val["pic"]
nclr = val["nodeClr"]
nodedatas = "{\"name\":\"%s\",\"title\":\"%s\",\"pic\":\"%s\",\"color\":\"%s\",\"r\":%s}" % (
name, title, pic, nclr, r)
nodedatastk.append(nodedatas)
gdata += ",".join(nodedatastk)
gdata += "],\"links\": ["
edgedatastk = []
for val in nm.readcsv(xxedge).getline(otype='dict'):
es = val["edgeSid"]
et = val["edgeEid"]
esize = val["edgesize"]
ecolor = val["edgecolor"]
edgedatas = "{\"source\":%s,\"target\":%s,\"length\":500,\"ewidth\":%s,\"color\":\"%s\"}" % (
es, et, esize, ecolor)
edgedatastk.append(edgedatas)
gdata += ','.join(edgedatastk)
gdata += "]}"
direct = ".attr('marker-end','url(#arrowhead)')"
if undirect:
direct = ""
nodeTemplate = '''
node
.append("circle")
.attr("r",function(d){return d.r/4;})
.attr("fill", function(d){return d.color;})
.append("title")
.text(function(d){return d.title;})
'''
nodemakeTemplate = '''
for(var i=0 ; i< graph.nodes.length;i++){
graph.nodes[i].id = i
}
'''
if pieDataFld != None:
nodeTemplate = '''
node.selectAll("path")
.data( function(d, i){
return pie(d.node);
})
.enter()
.append("svg:path")
.attr("d", arc)
.attr("fill", function(d, i) {
return color(d.data.group);
})
.append("title")
.text(function(d){{return d.data.title;}})
node.append("circle")
.attr("r",function(d){{return d.r/4;}})
.attr({
'fill': 'white'
})
.append("title")
.text(function(d){{return d.title;}});
'''
nodemakeTemplate = '''
for(var i=0 ; i< graph.nodes.length;i++){
var r = graph.nodes[i].r
for(var j=0 ; j< graph.nodes[i].node.length;j++){
graph.nodes[i].node[j]['r'] = r
}
graph.nodes[i].id = i
}
'''
elif picFld != None:
nodeTemplate = '''
node
.append("image")
.attr("height",function(d){return d.r;})
.attr("width",function(d){return d.r;})
.attr("x",function(d){return -1 * d.r/2; })
.attr("y",function(d){return -1 * d.r/2; })
.attr("xlink:href",function(d){return d.pic; })
.append("title")
.text(function(d){return d.title;})
'''
d3js_str = "<script type='text/javascript' src='http://d3js.org/d3.v3.min.js'></script>"
if offline:
d3js_str = "<script>%s<script>" % (vjs.ViewJs.d3jsMin())
outTemplate = '''
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
{d3js_str}
<style></style>
</head>
<body>
<script type="text/javascript">
var graph = {gdata} ;
var width = 4000,
height = 3000;
var color = d3.scale.category10();
{nodemakeTemplate};
for(var i=0 ; i< graph.links.length;i++){{
graph.links[i].id = i
}}
var pie = d3.layout.pie()
.sort(null)
.value(function(d) {{ return d.value; }});
var arc = d3.svg.arc()
.outerRadius( function(d){{ return d.data.r ; }})
.innerRadius( function(d){{ return d.data.r/2 ; }} );
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
d3.select("svg").append('defs').append('marker')
.attr({{'id':'arrowhead',
'viewBox':'-0 -5 10 10',
'refX':30,
'refY':0,
'orient':'auto-start-reverse',
'markerWidth':5,
'markerHeight':5,
'xoverflow':'visible'}})
.append('path')
.attr('d', 'M 0,-5 L 10 ,0 L 0,5')
.attr('fill', '#999')
.style('stroke','none');
var g = svg.append("g");
var node = g.selectAll(".node");
var link = g.selectAll(".link");
nodes = graph.nodes
links = graph.links
var force =
d3.layout.force()
.linkDistance(200)
.linkStrength(3.5)
.charge(-3500)
.gravity(0.1)
.friction(0.95)
.size([width, height])
.on("tick", function() {{
link
.attr("x1", function(d) {{ return d.source.x; }})
.attr("y1", function(d) {{ return d.source.y; }})
.attr("x2", function(d) {{ return d.target.x; }})
.attr("y2", function(d) {{ return d.target.y; }});
node
.attr("x", function(d) {{ return d.x; }})
.attr("y", function(d) {{ return d.y; }})
.attr("transform", function(d) {{ return "translate(" + d.x + "," + d.y + ")"}});
}});
node = node.data(nodes, function( d ) {{ return d.id; }} );
link = link.data(links, function( d ) {{ return d.id; }} );
link
.enter()
.append("line")
.attr("class", "link")
.style("stroke", function( d ) {{ return d.color; }} )
.style("stroke-width", function( d ) {{ return d.ewidth; }})
{direct}
node
.enter()
.append("g")
.attr("class", "node")
.style({{}})
.call(force.drag)
.on("contextmenu", function(nd) {{
d3.event.preventDefault();
force.stop()
nodes.splice( nd.index, 1 );
links = links.filter(function(nl) {{
return nl.source.index != nd.index && nl.target.index != nd.index;
}});
node = node.data(nodes, function( d ) {{ return d.id; }} );
node.exit().remove();
link = link.data( links, function( d ) {{ return d.id; }} );
link.exit().remove();
force.nodes(nodes)
.links(links)
.start();
}});
{nodeTemplate}
node
.append("text")
.attr("text-anchor", "middle")
.style("stroke", "black")
.text(function(d) {{ return d.name; }});
force.nodes(nodes)
.links(links)
.start();
</script>
</body>
</html>
'''.format(d3js_str=d3js_str,
gdata=gdata,
nodemakeTemplate=nodemakeTemplate,
direct=direct,
nodeTemplate=nodeTemplate)
html = sys.stdout
if not o == None:
html = open(o, "w")
html.write(outTemplate)
if not o == None:
html.close()
def __init__(self, nc, ni, col, order):
self.nc = nc
self.ni = ni
self.col = col
self.range = 0
self.min = 0
self.max = 0
self.order = order
if self.nc and self.ni:
if self.col == "category":
self.type = "category"
# preparing a color pallet
pallet = []
val = [
"FF", "80", "C0", "40", "E0", "60", "A0", "20", "F0", "70",
"B0", "30", "D0", "50", "90", "10"
]
for v in val:
pallet.append("%s0000" % (v))
pallet.append("00%s00" % (v))
pallet.append("0000%s" % (v))
pallet.append("%s%s00" % (v, v))
pallet.append("00%s%s" % (v, v))
pallet.append("%s00%s" % (v, v))
# read color field data and make a mapping table(data to pallet)
f = None
f <<= nm.mcut(f="%s:ckey" % (self.nc), i=self.ni)
f <<= nm.mdelnull(f="ckey")
f <<= nm.mcount(k="ckey", a="freq")
if self.order == "descend":
f <<= nm.mbest(s="freq%nr,ckey", fr=0,
size=96) #,o=#{xxcTable}
elif self.order == "ascend":
f <<= nm.mbest(s="freq%n,ckey", fr=0,
size=96) # o=#{xxcTable}"
else:
f <<= nm.mbest(s="ckey", fr=0, size=96) #o=#{xxcTable}"
self.cTable = {}
i = 0
for flds in f.getline(otype="dict"):
cK = flds["ckey"]
self.cTable[cK] = pallet[i]
i += 1
else:
self.type = "numeric"
ary = col.split(",")
if len(ary) != 2 or len(ary[0]) != 6 or len(ary[1]) != 6:
raise ValueError(
"col= takes two 6-digites HEX codes like FF0000,00FF00"
)
self.r0 = int(ary[0][0:2], 16)
self.g0 = int(ary[0][2:4], 16)
self.b0 = int(ary[0][4:6], 16)
self.r1 = int(ary[1][0:2], 16)
self.g1 = int(ary[1][2:4], 16)
self.b1 = int(ary[1][4:6], 16)
f = None
f <<= nm.mcut(f="%s:ckey" % (self.nc), i=self.ni)
f <<= nm.mdelnull(f="ckey")
f <<= nm.msummary(f="ckey", c="min,max")
xxcTable = f.run()
if len(xxcTable) > 0:
if len(xxcTable[0]) >= 2:
if xxcTable[0][1] != "":
self.min = float(xxcTable[0][1])
if xxcTable[0][2] != "":
self.max = float(xxcTable[0][2])
if xxcTable[0][1] != "" and xxcTable[0][2] != "":
self.range = self.max - self.min