def test6(showme=1, findallmatches=1):
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test6(
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells)
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells)
newvarsaffectedatwall = pp.varsAtWalls(threshnames, newwalldomains,
wallthresh, varnames)
wallinfo = makeWallInfo(newoutedges, newwalldomains, newvarsaffectedatwall)
wallinfo = pp.truncateExtendedWallGraph(booleanoutedges, newoutedges,
wallinfo)
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
patterns = pp.translatePatterns(varnames,
patternnames,
patternmaxmin,
cyclic=1)
solutions = [[(0, 5, 8, 9, 3, 1, 0), (0, 6, 11, 13, 16, 9, 3, 1, 0),
(0, 6, 12, 14, 8, 9, 3, 1, 0),
(0, 6, 12, 15, 16, 9, 3, 1, 0)],
[(4, 7, 13, 16, 9, 3, 1, 0, 4)], [(10, 7, 13, 16, 10)], None,
[(2, 7, 13, 16, 9, 3, 2)], None]
patterns = [p for pat in patterns for p in pat]
for p, s in zip(patterns, solutions):
match = matchPattern(p,
wallinfo,
cyclic=1,
findallmatches=findallmatches)
if s:
if showme and findallmatches: print set(match) == set(s)
if showme and not findallmatches: print match[0] in s
else:
if showme: print 'None' in match and 'Pattern' in match
def test5(showme=1, findallmatches=1):
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test5(
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells)
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells)
newvarsaffectedatwall = pp.varsAtWalls(threshnames, newwalldomains,
wallthresh, varnames)
wallinfo = makeWallInfo(newoutedges, newwalldomains, newvarsaffectedatwall)
wallinfo = pp.truncateExtendedWallGraph(booleanoutedges, newoutedges,
wallinfo)
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
patterns = pp.translatePatterns(varnames,
patternnames,
patternmaxmin,
cyclic=1)
match = matchPattern(patterns[0][0],
wallinfo,
cyclic=1,
findallmatches=findallmatches)
if showme and findallmatches:
print set(match) == set([(6, 0, 3, 4, 5, 10, 9, 8, 6),
(7, 1, 0, 3, 4, 5, 10, 9, 7),
(7, 2, 4, 5, 10, 9, 7)])
if showme and not findallmatches:
print match[0] in [(6, 0, 3, 4, 5, 10, 9, 8, 6),
(7, 1, 0, 3, 4, 5, 10, 9, 7),
(7, 2, 4, 5, 10, 9, 7)]
match = matchPattern(patterns[1][0],
wallinfo,
cyclic=1,
findallmatches=findallmatches)
if showme: print 'None' in match
def testtiming(iterates=5000):
outedges,walldomains,varsaffectedatwall,varnames,threshnames=tc.test6()
wallinfo = makeWallInfo(outedges,walldomains,varsaffectedatwall)
patternnames,patternmaxmin=fp.parsePatterns()
patterns=pp.translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)
for _ in range(iterates):
for p in patterns:
match = matchPattern(p,wallinfo,cyclic=1,findallmatches=1)
def testtiming(iterates=5000):
outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test6()
wallinfo = makeWallInfo(outedges, walldomains, varsaffectedatwall)
patternnames, patternmaxmin = fp.parsePatterns()
patterns = pp.translatePatterns(varnames, patternnames, patternmaxmin, cyclic=1)
for _ in range(iterates):
for p in patterns:
match = matchPattern(p, wallinfo, cyclic=1, findallmatches=1)
def test5():
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test5(
)
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
patterns = translatePatterns(varnames,
patternnames,
patternmaxmin,
cyclic=1)
print patterns == [[['mdd', 'umd', 'uum', 'Muu', 'dMu', 'ddM', 'mdd']],
[['mdd', 'umd', 'Mud', 'dum', 'dMu', 'ddM', 'mdd']]]
def test3():
domaingraph,domaincells,morseset,vertexmap,outedges,walldomains,varsaffectedatwall,varnames,threshnames=tc.test3()
extendedmorsegraph,extendedmorsecells=pp.makeExtendedMorseSetDomainGraph(vertexmap,morseset,domaingraph,domaincells)
print extendedmorsegraph==[[1,],[2,],[3,],[4,],[5,],[0,],[0,2,4],[1,3,5]]
print extendedmorsecells==domaincells[1:-1]+[domaincells[0]]+[domaincells[-1]]
newoutedges,wallthresh,newwalldomains,booleanoutedges=pp.makeWallGraphFromDomainGraph(len(vertexmap),extendedmorsegraph, extendedmorsecells)
print newoutedges==outedges+[(0,),(2,),(4,),(1,),(3,),(5,)]
print newwalldomains==walldomains+ [(1,0.5,0.5),(0.5,0.5,1),(0.5,1,0.5)] + [(1.5,1,1.5),(1,1.5,1.5),(1.5,1.5,1)]
print wallthresh==[2,0,1,2,0,1,0,2,1,1,0,2]
print pp.varsAtWalls(threshnames,newwalldomains,wallthresh,varnames)==varsaffectedatwall+[1,0,2,2,1,0]
patternnames=[['X','Z','Y','X','Y','Z'],['Z','X','Y','Y','X','Z']]
patternmaxmin=[['min','max','min','max','max','min'],['max','min','min','max','max','min']]
patterns=translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)
print patterns==[[['mdu','udM','umd','Mud','dMd','ddm','mdu']],[['ddM','mdd','umd','uMd','Mdd','ddm','ddM']]]
patternnames,patternmaxmin,originalpatterns=fp.parsePatterns()
print translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)==[[['udm','Mdu','dmu','duM','mud','uMd','udm']],[['dum','muu','uMu','umu','uuM','Mud','dum']]]
def test3():
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test3(
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells)
print extendedmorsegraph == [[
1,
], [
2,
], [
3,
], [
4,
], [
5,
], [
0,
], [0, 2, 4], [1, 3, 5]]
print extendedmorsecells == domaincells[1:-1] + [domaincells[0]
] + [domaincells[-1]]
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells)
print newoutedges == outedges + [(0, ), (2, ), (4, ), (1, ), (3, ), (5, )]
print newwalldomains == walldomains + [(1, 0.5, 0.5), (0.5, 0.5, 1),
(0.5, 1, 0.5)] + [(1.5, 1, 1.5),
(1, 1.5, 1.5),
(1.5, 1.5, 1)]
print wallthresh == [2, 0, 1, 2, 0, 1, 0, 2, 1, 1, 0, 2]
print pp.varsAtWalls(threshnames, newwalldomains, wallthresh,
varnames) == varsaffectedatwall + [1, 0, 2, 2, 1, 0]
patternnames = [['X', 'Z', 'Y', 'X', 'Y', 'Z'],
['Z', 'X', 'Y', 'Y', 'X', 'Z']]
patternmaxmin = [['min', 'max', 'min', 'max', 'max', 'min'],
['max', 'min', 'min', 'max', 'max', 'min']]
patterns = translatePatterns(varnames,
patternnames,
patternmaxmin,
cyclic=1)
print patterns == [[['mdu', 'udM', 'umd', 'Mud', 'dMd', 'ddm', 'mdu']],
[['ddM', 'mdd', 'umd', 'uMd', 'Mdd', 'ddm', 'ddM']]]
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
print translatePatterns(
varnames, patternnames, patternmaxmin,
cyclic=1) == [[['udm', 'Mdu', 'dmu', 'duM', 'mud', 'uMd', 'udm']],
[['dum', 'muu', 'uMu', 'umu', 'uuM', 'Mud', 'dum']]]
def test4():
domaingraph,domaincells,morseset,vertexmap,outedges,walldomains,varsaffectedatwall,varnames,threshnames=tc.test4()
extendedmorsegraph,extendedmorsecells=pp.makeExtendedMorseSetDomainGraph(vertexmap,morseset,domaingraph,domaincells)
print extendedmorsegraph==[[6,1],[2,4],[5,],[0,],[3,],[4,],[]]
print extendedmorsecells==domaincells[3:]+[domaincells[0]]
newoutedges,wallthresh,newwalldomains,booleanoutedges=pp.makeWallGraphFromDomainGraph(len(vertexmap),extendedmorsegraph, extendedmorsecells)
print newoutedges==[(),(2,3),(4,),(6,),(7,),(0,1),(5,),(6,)]
print newwalldomains==[(1,2.5)] +walldomains
print wallthresh==[0,1,1,0,0,0,1,1]
print pp.varsAtWalls(threshnames,newwalldomains,wallthresh,varnames)==[0]+varsaffectedatwall
patternnames=[['X1','X2','X1','X2'],['X1','X1','X2','X2']]
patternmaxmin=[['min','min','max','max'],['max','min','min','max']]
patterns=translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)
print patterns==[[['md','um','Mu','dM','md']],[['Md','md','um','uM','Md']]]
patternnames,patternmaxmin,originalpatterns=fp.parsePatterns()
print patternnames==[['X2', 'X1', 'X2', 'X1'], ['X2', 'X2', 'X1', 'X1']]
print patternmaxmin==[['max', 'min', 'min', 'max'], ['max', 'min', 'min', 'max']]
print translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)==[[['dM','md','um','Mu','dM']],[['dM','dm','mu','Mu','dM']]]
def preprocess(fname1='dsgrn_output.json',fname2='dsgrn_domaingraph.json',fname3='dsgrn_domaincells.json',pname='patterns.txt',cyclic=1):
# read input files
varnames,threshnames,morsedomgraph,morsecells,vertexmap=fp.parseMorseSet(fname1)
domaingraph=fp.parseDomainGraph(fname2)
domaincells=fp.parseDomainCells(fname3)
patternnames,patternmaxmin,originalpatterns=fp.parsePatterns(pname)
# put max/min patterns in terms of the alphabet u,m,M,d
patterns=translatePatterns(varnames,patternnames,patternmaxmin,cyclic=cyclic)
# translate domain graph into wall graph
extendedmorsegraph,extendedmorsecells=makeExtendedMorseSetDomainGraph(vertexmap,morsecells,domaingraph,domaincells)
outedges,wallthresh,walldomains,booleanoutedges=makeWallGraphFromDomainGraph(len(vertexmap),extendedmorsegraph, extendedmorsecells)
# record which variable is affected at each wall
varsaffectedatwall=varsAtWalls(threshnames,walldomains,wallthresh,varnames)
# make wall labels
wallinfo = wl.makeWallInfo(outedges,walldomains,varsaffectedatwall)
# truncate back to Morse wall graph
wallinfo = truncateExtendedWallGraph(booleanoutedges,outedges,wallinfo)
return patterns, originalpatterns, wallinfo
def test3(showme=1, findallmatches=1):
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = (
tc.test3()
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells
)
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells
)
newvarsaffectedatwall = pp.varsAtWalls(threshnames, newwalldomains, wallthresh, varnames)
wallinfo = makeWallInfo(newoutedges, newwalldomains, newvarsaffectedatwall)
wallinfo = pp.truncateExtendedWallGraph(booleanoutedges, newoutedges, wallinfo)
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
patterns = pp.translatePatterns(varnames, patternnames, patternmaxmin, cyclic=1)
match = matchPattern(patterns[0][0], wallinfo, cyclic=1, findallmatches=findallmatches)
if showme:
print match == [(5, 0, 1, 2, 3, 4, 5)]
match = matchPattern(patterns[1][0], wallinfo, cyclic=1, findallmatches=findallmatches)
if showme:
print "None" in match
def test6(showme=1, findallmatches=1):
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = (
tc.test6()
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells
)
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells
)
newvarsaffectedatwall = pp.varsAtWalls(threshnames, newwalldomains, wallthresh, varnames)
wallinfo = makeWallInfo(newoutedges, newwalldomains, newvarsaffectedatwall)
wallinfo = pp.truncateExtendedWallGraph(booleanoutedges, newoutedges, wallinfo)
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
patterns = pp.translatePatterns(varnames, patternnames, patternmaxmin, cyclic=1)
solutions = [
[
(0, 5, 8, 9, 3, 1, 0),
(0, 6, 11, 13, 16, 9, 3, 1, 0),
(0, 6, 12, 14, 8, 9, 3, 1, 0),
(0, 6, 12, 15, 16, 9, 3, 1, 0),
],
[(4, 7, 13, 16, 9, 3, 1, 0, 4)],
[(10, 7, 13, 16, 10)],
None,
[(2, 7, 13, 16, 9, 3, 2)],
None,
]
patterns = [p for pat in patterns for p in pat]
for p, s in zip(patterns, solutions):
match = matchPattern(p, wallinfo, cyclic=1, findallmatches=findallmatches)
if s:
if showme and findallmatches:
print set(match) == set(s)
if showme and not findallmatches:
print match[0] in s
else:
if showme:
print "None" in match and "Pattern" in match
def test4():
domaingraph, domaincells, morseset, vertexmap, outedges, walldomains, varsaffectedatwall, varnames, threshnames = tc.test4(
)
extendedmorsegraph, extendedmorsecells = pp.makeExtendedMorseSetDomainGraph(
vertexmap, morseset, domaingraph, domaincells)
print extendedmorsegraph == [[6, 1], [2, 4], [
5,
], [
0,
], [
3,
], [
4,
], []]
print extendedmorsecells == domaincells[3:] + [domaincells[0]]
newoutedges, wallthresh, newwalldomains, booleanoutedges = pp.makeWallGraphFromDomainGraph(
len(vertexmap), extendedmorsegraph, extendedmorsecells)
print newoutedges == [(), (2, 3), (4, ), (6, ), (7, ), (0, 1), (5, ),
(6, )]
print newwalldomains == [(1, 2.5)] + walldomains
print wallthresh == [0, 1, 1, 0, 0, 0, 1, 1]
print pp.varsAtWalls(threshnames, newwalldomains, wallthresh,
varnames) == [0] + varsaffectedatwall
patternnames = [['X1', 'X2', 'X1', 'X2'], ['X1', 'X1', 'X2', 'X2']]
patternmaxmin = [['min', 'min', 'max', 'max'],
['max', 'min', 'min', 'max']]
patterns = translatePatterns(varnames,
patternnames,
patternmaxmin,
cyclic=1)
print patterns == [[['md', 'um', 'Mu', 'dM', 'md']],
[['Md', 'md', 'um', 'uM', 'Md']]]
patternnames, patternmaxmin, originalpatterns = fp.parsePatterns()
print patternnames == [['X2', 'X1', 'X2', 'X1'], ['X2', 'X2', 'X1', 'X1']]
print patternmaxmin == [['max', 'min', 'min', 'max'],
['max', 'min', 'min', 'max']]
print translatePatterns(varnames, patternnames, patternmaxmin,
cyclic=1) == [[['dM', 'md', 'um', 'Mu', 'dM']],
[['dM', 'dm', 'mu', 'Mu', 'dM']]]
def test6():
domaingraph,domaincells,morseset,vertexmap,outedges,walldomains,varsaffectedatwall,varnames,threshnames=tc.test6()
patternnames,patternmaxmin,originalpatterns=fp.parsePatterns()
patterns=translatePatterns(varnames,patternnames,patternmaxmin,cyclic=1)
print patterns==[[['umu','Muu','duM','dMd','mdd','udm','umu']],[['uuM','uum','Muu','duM','dMd','mdd','udm','umu','uuM']],[['mud','uum','Muu','duM','mud'],['mdd','udm','Mdu','ddM','mdd']],[['umd','uum','Muu','duM','dMd','mdd','umd']],[['dmd','dum','muu','uuM','uMd','Mdd','dmd']]]