def run_homfly(link_set):
"""
# determines whether a harddrive is plugged in
question = input("Is your external hard drive connected? (yes/no) ")
if question == "yes":
pass
else:
raise Exception("You need a hard drive for this computation!")
"""
if os.path.isfile("/media/alexander/HollisExt30/master_link_index.txt"):
H = file_to_dict(
"/media/alexander/HollisExt30/master_link_index.txt").values()
else:
H = []
#if os.path.isfile("/media/alexander/HollisExt30/master_link_index.txt"):
z = open(link_set)
count = 0
while True:
count += 1
if count % 10000 == 0:
print(count)
try:
new_knot = PlanarDiagram.read(z)
homfly = str(new_knot.homfly())
if homfly in H:
homfly_results(str(H.index(homfly)), new_knot)
else:
H.append(homfly)
master_index(str(H.index(homfly)), homfly)
homfly_results(str(H.index(homfly)), new_knot)
except:
break
def counter(file_name):
fil = open(file_name)
count = 0
while 1:
a = PlanarDiagram.read(fil)
count += 1
print count
def run_homfly(link_set):
'''
runs homefly for each .pdstor
determines whether a harddrive is plugged in
question = input("Is your external hard drive connected? (yes/no) ")
if question == "yes":
pass
else:
raise Exception("You need a hard drive for this computation!")
'''
if os.path.isfile("/home/hollis/dev/KnotModels/link_code/test2/master_link_index.txt"):
H = file_to_dict("/home/hollis/dev/KnotModels/link_code/test2/master_link_index.txt")
else:
H = {}
#if os.path.isfile("/media/alexander/HollisExt30/master_link_index.txt"):
z = open(link_set)
count = 0
while True:
if len(H.keys()) == 0:
mx = 0
if len(H.keys()) != 0:
mx = int(max(H.keys()))
count += 1
if count %10000 == 0:
print(count)
try:
shadows = []
shad = PlanarDiagram.read(z)
num_cross = shad.ncross
nums = 2**num_cross
typ = "{0:0" + str(num_cross) + "b}"
cross_types = []
for b in range(nums):
cross_types.append(typ.format(b))
for c in range(len(cross_types)):
knot = copy.copy(shad)
for d in range(num_cross):
knot.crossings[d].sign = int(cross_types[c][d])
shadows.append(knot)
for iter1 in range(len(shadows)):
new_knot = shadows[iter1]
homfly = str(new_knot.homfly())
if homfly in H.values():
homfly_results(str(H.values().index(homfly)), new_knot)
else:
mx += 1
H[mx] = homfly
master_index(str(H.values().index(homfly)), homfly)
homfly_results(str(H.values().index(homfly)), new_knot)
except:
z.close()
break
def vred(file_path):
z = open(file_path)
pdcodes = []
while 1:
try:
pdcodes.append(PlanarDiagram.read(z))
except:
break
human_reduced = []
pl0 = pdcodes[0].as_spherogram().view()
keep = [pdcodes.pop(0)]
for a in range(len(pdcodes)):
if type(pdcodes[a]) == int:
continue
pl = pdcodes[a].as_spherogram().view()
delete = raw_input("isotopic? y/n : ")
pl.done()
if delete == 'y':
human_reduced.append(pdcodes[a])
if delete == 'n':
keep.append(pdcodes[a])
pl0.done()
f1 = open(
file_path[0:len(file_path) - 31] + "human_reduced/" +
file_path[len(file_path) - 31:len(file_path)], "a")
f2 = open(file_path[0:len(file_path) - 14] + ".pdstor", "a")
for a in human_reduced:
a.write(f1)
for a in keep:
a.write(f2)
os.remove(file_path)
f1.close()
z.close()
f2.close()
def isometry_reduce(file_path):
z = open(file_path)
pdcodes = []
while 1:
try:
pdcodes.append(PlanarDiagram.read(z))
except:
break
z.close()
# Now I have all pd in ram
splittable = []
non_split = []
isom_un = []
non_un = []
print len(pdcodes)
for a in pdcodes:
pot = a.simplify()
if len(pot) != 1:
splittable.append(a)
if len(pot) == 1:
knot = pot[0]
knot.regenerate()
non_split.append(knot)
pdlist = list(non_split)
if len(non_split) != 0:
isom_un.append(pdlist[0])
pdlist[0] = 0
for a in range(len(pdlist)):
for b in range(len(isom_un)):
if type(pdlist[a]) != int and pdlist[a].isomorphic(isom_un[b]):
non_un.append(pdlist[a])
pdlist[a] = 0
if type(pdlist[a]) != int and b == len(isom_un) - 1:
isom_un.append(pdlist[a])
pdlist[a] = 0
f1 = open(file_path[0:len(file_path) - 7] + "_unique.pdstor", "a")
f2 = open(
file_path[0:len(file_path) - 24] + "non_unique/" +
file_path[len(file_path) - 24:len(file_path) - 7] + "_isom.pdstor",
"a")
splitfile = open(
file_path[0:len(file_path) - 24] + "non_unique/" +
file_path[len(file_path) - 24:len(file_path) - 7] +
"_splittable.pdstor", "a")
os.remove(file_path)
for a in isom_un:
a.write(f1)
for a in non_un:
a.write(f2)
for a in splittable:
a.write(splitfile)
f1.close()
f2.close()
splitfile.close()
return
def num_of_diagrams(filename):
count = 0
z = open(filename)
print "Counting..."
while 1:
try:
a = PlanarDiagram.read(z)
count += 1
except:
break
if count % 10000 == 0:
print "Passed ", count, " diagrams."
z.close()
return count
def run_simplify(file_path, length):
pdcodes = []
z = open(file_path)
while 1:
try:
pdcodes.append(PlanarDiagram.read(z))
except:
break
z.close()
if len(pdcodes) == 1 and length != 24:
f1 = open(file_path[0:len(file_path) - 14] + ".pdstor", "a")
pdcodes[0].write(f1)
f1.close()
os.remove(file_path)
if len(pdcodes) == 0:
os.remove(file_path)
return
def random_diagram_parser(string):
name = "/home/hollis/dev/randomdiagram/src/" + string
pdcode = open(name)
pdcode.readline()
dest = open(
"/home/hollis/dev/KnotModels/link_code/shadows/" + string[0:1] +
".pdstor", "a")
count = 1
while 1:
try:
diag = PlanarDiagram.read(pdcode)
if diag.ncomps > 1:
diag.write(dest)
except:
count += 1
if count > 10:
break
pdcode.close()
dest.close()
print "Finished : "
j = a
fil1 = open(name)
num = 1
all_links = []
#fil = open("/media/alexander/HollisExt30/link_data/data/" + str(a) + "/"+ str(a)+"_links.pdstor","a")
fil = open("/media/hollis/HollisExtTB/link_data/data/" + str(a) + "/"+ str(a)+"_links.pdstor","a")
count = 0
print "Starting"
while num:
try:
a = PlanarDiagram.read(fil1)
num_cross = a.ncross
nums = 2**num_cross
typ = "{0:0" + str(num_cross) + "b}"
cross_types = []
for b in range(nums):
cross_types.append(typ.format(b))
for c in range(len(cross_types)):
for d in range(num_cross):
a.crossings[d].sign = int(cross_types[c][d])
a.write(fil)
count += 1
if count%1000 == 0:
print "finished " + str(count)
except EOFError:
num = 0
def link_reduce(homfly):
z = open(path + "homfly_storage/" + homfly)
split_file = open(
path + "reduced_homfly_storage" + "/splittable_" + homfly, 'a')
unsplit_file = open(
path + "reduced_homfly_storage" + "/unsplittable_" + homfly, 'a')
count = 0
knots = []
while True:
count += 1
if count % 10000 == 0:
print(count)
try:
knot = PlanarDiagram.read(z)
linking_num = []
is_written = 0
for comp1 in range(knot.ncomps):
for comp2 in range(knot.ncomps):
ln = knot.linking_number(comp1, comp2)
if comp1 != comp2:
linking_num.append(ln)
if linking_num.count(0) == 0:
num_isotopies = 0
if len(knots) == 0:
knots.append(knot)
continue
for a in knots:
if a.isotopic(knot):
num_isotopies += 1
break
if num_isotopies == 0:
knots.append(knot)
# knots.write(unsplit_file)
is_written = 1
if linking_num.count(0) != 0:
if len(knot.simplify()) == 1:
num_isotopies = 0
if len(knots) == 0:
knots.append(knot)
continue
for a in knots:
if a.isotopic(knot):
num_isotopies += 1
break
if num_isotopies == 0:
knots.append(knot)
# knots.write(unsplit_file)
is_written = 1
if (not is_written):
knot.write(split_file)
except:
break
knots.write(unsplit_file)
# print "Number of knots :", len(knots)
# reduced = isotopic_reduce2(knots)
split_file.close()
unsplit_file.close()