def pois_fixposition(mat):
origina_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)] for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_p", f_p
#print "f_s", f_s
#print "jmat", origina_j
for i in range(n_p):
for j in range(i + 1, n_p):
test_s = origina_j[i][j]
rate_c = f_p[i] * f_p[j]
#print "test_s", test_s
#print "rate_c", rate_c
total = 0
#total = (1- rate_c)**n_s
for t in range(test_s + 1): #change!
#print "t, test_s, scm.comb", t, test_s, scm.comb(n_s, t)
total += scm.comb(n_s, t) * (rate_c**t) * (
(1 - rate_c)**(n_s - t))
#print "i, j, total", i, j, total
#print "decimal", Decimal(str(total))
#print "1 minus", 1-total
#print "multiple", total*1.0
if 1.0 - (0.1)**8 <= total <= 1.0 + (0.1)**8:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
ta = float(1.0 - total)
#print "ta", ta
#print "to", total
p_mat[i][j] = -math.log10(ta)
p_mat[j][i] = -math.log10(ta)
return p_mat
def pois_fixposition(mat):
origina_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)]for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_p", f_p
#print "f_s", f_s
#print "jmat", origina_j
for i in range(n_p):
for j in range(i+1, n_p):
test_s = origina_j[i][j]
rate_c = f_p[i]*f_p[j]
#print "test_s", test_s
#print "rate_c", rate_c
total = 0
#total = (1- rate_c)**n_s
for t in range(test_s+1):#change!
#print "t, test_s, scm.comb", t, test_s, scm.comb(n_s, t)
total += scm.comb(n_s, t) * (rate_c**t) * ((1-rate_c)**(n_s -t))
#print "i, j, total", i, j, total
#print "decimal", Decimal(str(total))
#print "1 minus", 1-total
#print "multiple", total*1.0
if 1.0-(0.1)**8 <= total <= 1.0+(0.1)**8:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
ta = float(1.0 - total)
#print "ta", ta
#print "to", total
p_mat[i][j] = -math.log10(ta)
p_mat[j][i] = -math.log10(ta)
return p_mat
def pois_fixsample_byR(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)] for i in range(n_p)]
f_p, f_s = make_freq(mat)
#print "f_s", f_s
list_rate = [x**2 for x in f_s]
f = open("b.txt", "w")
b = [str(x) + " " for x in list_rate]
b.append("\n")
#print "b", b
f.writelines(b)
f.close()
for i in range(n_p):
for j in range(i + 1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
cmd = "R --vanilla --args " + str(
test_s) + " < ./fixsample_poisson.R"
os.system(cmd)
f1 = open("s.txt", "r")
l = f1.readline()
#print "l", l
total = float(l)
#print "test_s", test_s
#print "*******************************************"
#print "total", total
if 1.0 - (0.1)**15 <= total <= 1.0 + (0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1 - total)
p_mat[j][i] = -math.log10(1 - total)
return p_mat
def pois_fixsample_byR(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)]for i in range(n_p)]
f_p, f_s = make_freq(mat)
#print "f_s", f_s
list_rate = [x**2 for x in f_s]
f = open("b.txt", "w")
b = [str(x)+" " for x in list_rate]
b.append("\n")
#print "b", b
f.writelines(b)
f.close()
for i in range(n_p):
for j in range(i+1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
cmd = "R --vanilla --args "+str(test_s)+" < ./fixsample_poisson.R"
os.system(cmd)
f1 = open("s.txt", "r")
l = f1.readline()
#print "l", l
total = float(l)
#print "test_s", test_s
#print "*******************************************"
#print "total", total
if 1.0-(0.1)**15 <= total <= 1.0+(0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1-total)
p_mat[j][i] = -math.log10(1-total)
return p_mat
def pois_fixsample_bylessR(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)] for i in range(n_p)]
f_p, f_s = make_freq(mat)
#print "f_s", f_s
list_rate = [x**2 for x in f_s]
f = open("b.txt", "w")
b = [str(x) + " " for x in list_rate]
b.append("\n")
#print "b", b
f.writelines(b)
f.close()
tests_s = []
for i in range(n_p):
for j in range(i + 1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
tests_s.append(test_s)
f = open("tests.txt", "w")
f.write(" ".join([str(x) for x in tests_s]))
f.close()
cmd = "R --vanilla --args " + str(test_s) + " < ./fixsample_poisson_less.R"
os.system(cmd)
f1 = open("s.txt", "r")
l = []
for line in f1:
l += line.replace('\n', '').split(' ')
f1.close()
list_float = [float(x) for x in l]
#print "l", l
#total = float(l)
#print "test_s", test_s
#print "*******************************************"
#print "total", total
for i in range(n_p):
for j in range(i + 1, n_p):
total = list_float.pop(0)
if 1.0 - (0.1)**15 <= total <= 1.0 + (0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1 - total)
p_mat[j][i] = -math.log10(1 - total)
return p_mat
def pois_fixsample_bylessR(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)]for i in range(n_p)]
f_p, f_s = make_freq(mat)
#print "f_s", f_s
list_rate = [x**2 for x in f_s]
f = open("b.txt", "w")
b = [str(x)+" " for x in list_rate]
b.append("\n")
#print "b", b
f.writelines(b)
f.close()
tests_s = []
for i in range(n_p):
for j in range(i+1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
tests_s.append(test_s)
f = open("tests.txt", "w")
f.write(" ".join([str(x) for x in tests_s]))
f.close()
cmd = "R --vanilla --args "+str(test_s)+" < ./fixsample_poisson_less.R"
os.system(cmd)
f1 = open("s.txt", "r")
l = []
for line in f1:
l += line.replace('\n','').split(' ')
f1.close()
list_float = [float(x) for x in l]
#print "l", l
#total = float(l)
#print "test_s", test_s
#print "*******************************************"
#print "total", total
for i in range(n_p):
for j in range(i+1, n_p):
total = list_float.pop(0)
if 1.0-(0.1)**15 <= total <= 1.0+(0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1-total)
p_mat[j][i] = -math.log10(1-total)
return p_mat
def pois_fixsample(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)] for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_s", f_s
sys.stdout.flush()
for i in range(n_p):
print "n_p", n_p
sys.stdout.flush()
for j in range(i + 1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
#print "test_s", test_s
s_list = [x for x in range(n_s)]
total = 1
for t in range(n_s):
total *= (1 - (f_s[t])**2) #when 0
#print "first total", total
for t in range(1, test_s + 1): #change test_s
mi_total = 0
#print "s_list", s_list
#print "i,j,t", i,j,t
for c in combinations(s_list, t):
c = list(c)
remain_l = list(set(s_list) - set(c))
#print "c", c
#print "remain",remain_l
subtotal = 1
for s in range(t):
subtotal *= (f_s[c[s]]**2)
for s in range(n_s - t):
subtotal *= (1 - (f_s[remain_l[s]])**2)
mi_total += subtotal
#print "middle", t, mi_total
total += mi_total
#print "total", total
#print "1-total", 1-total
#print "*******************************************"
#print "total", total
if 1.0 - (0.1)**15 <= total <= 1.0 + (0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1 - total)
p_mat[j][i] = -math.log10(1 - total)
return p_mat
def pois_fixsample(mat):
original_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)]for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_s", f_s
sys.stdout.flush()
for i in range(n_p):
print "n_p", n_p
sys.stdout.flush()
for j in range(i+1, n_p):
#print "*******************************************"
test_s = original_j[i][j]
#print "test_s", test_s
s_list = [x for x in range(n_s)]
total = 1
for t in range(n_s):
total *= (1 - (f_s[t])**2)#when 0
#print "first total", total
for t in range(1, test_s+1):#change test_s
mi_total = 0
#print "s_list", s_list
#print "i,j,t", i,j,t
for c in combinations(s_list, t):
c = list(c)
remain_l = list(set(s_list) - set(c))
#print "c", c
#print "remain",remain_l
subtotal = 1
for s in range(t):
subtotal *= (f_s[c[s]]**2)
for s in range(n_s -t):
subtotal *= (1- (f_s[remain_l[s]])**2)
mi_total += subtotal
#print "middle", t, mi_total
total += mi_total
#print "total", total
#print "1-total", 1-total
#print "*******************************************"
#print "total", total
if 1.0-(0.1)**15 <= total <= 1.0+(0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
p_mat[i][j] = -math.log10(1-total)
p_mat[j][i] = -math.log10(1-total)
return p_mat
def pois_fixposition_byR(mat, roop_n):
origina_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)] for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_p", f_p
print "f_s", f_s
#print "jmat", origina_j
for i in range(n_p):
for j in range(i + 1, n_p):
#a = f_p[i]*f_p[j]
f = open("a.txt", "w")
a = str(f_p[i] * f_p[j])
print "a", a
f.writelines(a)
f.close()
print "a", a
test_s = origina_j[i][j]
print "test_s", test_s
cmd = "R --vanilla --args " + str(test_s) + " " + str(
a) + " " + str(
n_s
) + " " + roop_n + " < /home/ayada/cell/fixposition_poison.R"
os.system(cmd)
fname = "p" + roop_n + ".txt"
f1 = open(fname, "r")
l = f1.readline()
print "l", l
total = float(l)
print "total", total
if 1.0 - (0.1)**15 <= total <= 1.0 + (0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
ta = float(1.0 - total)
p_mat[i][j] = -math.log10(ta)
p_mat[j][i] = -math.log10(ta)
return p_mat
def pois_fixposition_byR(mat, roop_n):
origina_j = makej(mat)
n_p = len(mat)
n_s = len(mat[0])
p_mat = [[0 for i in range(n_p)]for i in range(n_p)]
f_p, f_s = make_freq(mat)
print "f_p", f_p
print "f_s", f_s
#print "jmat", origina_j
for i in range(n_p):
for j in range(i+1, n_p):
#a = f_p[i]*f_p[j]
f = open("a.txt", "w")
a = str(f_p[i]*f_p[j])
print "a", a
f.writelines(a)
f.close()
print "a" , a
test_s = origina_j[i][j]
print "test_s" , test_s
cmd = "R --vanilla --args "+str(test_s)+" "+str(a)+" "+str(n_s)+" "+roop_n+" < /home/ayada/cell/fixposition_poison.R"
os.system(cmd)
fname = "p"+roop_n+".txt"
f1 = open(fname, "r")
l = f1.readline()
print "l", l
total = float(l)
print "total", total
if 1.0-(0.1)**15 <= total <= 1.0+(0.1)**15:
p_mat[i][j] = 1
p_mat[j][i] = 1
else:
ta = float(1.0 - total)
p_mat[i][j] = -math.log10(ta)
p_mat[j][i] = -math.log10(ta)
return p_mat
