def net_ggsvd(name=nu.default_name, reset=0):
hardcopy = False
try:
if reset:
raise Exception("compute")
return nw.readnet(name, hardcopy=hardcopy)
except Exception as e:
if e.args[0] != "compute":
raise Exception()
nw.claim_reset()
ggn = nu.net_genegene_norm(reset=mod(reset, 2))
U, S, Vh = lin.svd(ggn)
V = Vh.T
dosave = (U, S, V)
nw.writenet(name, dosave, hardcopy=hardcopy)
print """
Ran ggsvd.
No hardcopies have been saved yet"""
if reset:
net_ggsvd_U(reset=2)
net_ggsvd_V(reset=2)
net_ggsvd_S(reset=2)
print """
...saved hardcopies of U,S,V
"""
return dosave
def draw_ggn():
ggn = nu.net_genegene_norm()
f = plt.figure(cfig)
f.clear()
ax = f.add_axes([0,0,1,1])
sums = np.sum(ggn,0)
ax.plot(sums)
def smear_ggn():
ggn = nu.net_genegene_norm()
img = array(ggn)
s = shape(img)
for i in range(s[1]):
img[:,i] = np.sort(img[:,i])[::-1]/ np.max(img[:,i])
sums = np.sum(img ** 2,0)
img = img[:, np.argsort(sums)[::-1]]
draw_smear(img[::xskip,::yskip])
def net_cluster_ggn(k = k, reset = 0):
hardcopy = True
try:
if reset: raise Exception('compute')
out,sxs = nw.rn2(name, hardcopy = hardcopy)
if not sxs: raise Exception()
except Exception as e:
if e.args[0] != 'compute': raise Exception()
nw.claim_reset()
gg = nu.net_genegene_norm(reset = mod(reset,2))
kmeans = mlpy.Kmeans(k)
clustered = kmeans.compute(gg[0:maxgenes,:])
means = kmeans.means
out = (clustered,means)
nw.wn2(name, (clustered, means) ,hardcopy = hardcopy)
return out