def plot_line(gr, ax, key):
ax.cla()
ax.set_title(' {0} vs score'.format(key[0]))
z = np.array([np.sum(list(p.dtc.scores.values())) for p in gr])
x = np.array([p.dtc.attrs[key[0]] for p in gr])
ax.plot(x, z)
ax.set_xlim(np.min(x), np.max(x))
ax.set_ylim(np.min(z), np.max(z))
return ax
def check_line(line, gr, newrange, key):
# Is this a concave down shape (optima in the middle)
# Or is the most negative value on an edge?
# if it's on the edge calculate a new parameter value to explore
range_adj = False
min_ = np.min(line)
cl = [g.dtc.attrs[key] for g in gr]
new = None
index = None
new_param_val = None
if line[0] == min_:
attrs = gr[0].dtc.attrs[key]
# quantity may not be negative yet
# don't force it to be straight away
# avoided forcing rapid sign reversal by keeping old value as an offset
remin = attrs - 10 * np.abs(attrs)
if remin == 0.0:
remin = -1.0
cl.insert(0, remin)
cl = sorted(cl)
newrange[key] = cl
range_adj = True
new_param_val = cl[0]
index = 0
if line[-1] == min_:
attrs = gr[-1].dtc.attrs[key]
# quantity might not be positve yet
# don't force it to be straight away
# avoided forcing rapid sign reversal by keeping old value as an offset
remax = attrs + np.abs(attrs) * 10
if remax == 0.0:
remax = 1.0
cl.append(remax)
cl = sorted(cl)
newrange[key] = cl
range_adj = True
new_param_val = cl[-1]
index = -1
return (newrange, range_adj, new_param_val, index)
def check_line(line,newrange):
range_adj = False
keys = keys[0]
min_ = np.min(line)
print(min_,line[0],line[1],'diff?')
if line[0] == min_:
#print('hit')
attrs = gr[0].dtc.attrs[keys]
remin = - np.abs(attrs)*10
remax = np.abs(gr[-1].dtc.attrs[keys])*10
nr = np.linspace(remin,remax,10)
newrange[keys] = nr
range_adj = True
if line[-1] == min_:
#print('hit')
attrs = gr[-1].dtc.attrs[keys]
remin = - np.abs(attrs)*10
remax = np.abs(gr[-1].dtc.attrs[keys])*10
nr = np.linspace(remin,remax,10)
newrange[keys] = nr
range_adj = True
def check_line(line, gr, newrange):
range_adj = False
key = list(newrange.keys())[0]
#keys = keys[0]
min_ = np.min(line)
print(min_, line[0], line[1], 'diff?')
if line[0] == min_:
#print('hit')
attrs = gr[0].dtc.attrs[key]
remin = -np.abs(attrs) * 10
remax = np.abs(gr[-1].dtc.attrs[key]) * 10
nr = np.linspace(remin, remax, 3)
newrange[key] = nr
range_adj = True
if line[-1] == min_:
#print('hit')
attrs = gr[-1].dtc.attrs[key]
remin = -np.abs(attrs) * 10
remax = np.abs(gr[-1].dtc.attrs[key]) * 10
nr = np.linspace(remin, remax, 3)
newrange[key] = nr
range_adj = True
return (newrange, range_adj)
def evidence(matrix,hof):
dim = np.shape(matrix)[0]
print(dim)
cnt = 0
fig,ax = plt.subplots(dim,dim,figsize=(10,10))
flat_iter = []
newrange = {}
for i,k in enumerate(matrix):
for j,r in enumerate(k):
keys = list(r[0])
gr = r[1]
line = [ np.sum(list(g.dtc.scores.values())) for g in gr]
print(line)
if i==j:
keys = keys[0]
min_ = np.min(line)
print(min_,line[0],line[1],'diff?')
if line[0] == min_:
print('hit')
attrs = gr[0].dtc.attrs[keys]
remin = - np.abs(attrs)*10
remax = np.abs(gr[-1].dtc.attrs[keys])*10
nr = np.linspace(remin,remax,10)
newrange[keys] = nr
if line[-1] == min_:
print('hit')
attrs = gr[-1].dtc.attrs[keys]
remin = - np.abs(attrs)*10
remax = np.abs(gr[-1].dtc.attrs[keys])*10
nr = np.linspace(remin,remax,10)
newrange[keys] = nr
print(newrange,'newrange')
return newrange
def grids(hof, tests, params):
dim = len(hof[0].dtc.attrs.keys())
flat_iter = iter([(i, ki, j, kj)
for i, ki in enumerate(hof[0].dtc.attrs.keys())
for j, kj in enumerate(hof[0].dtc.attrs.keys())])
matrix = [[0 for x in range(dim)] for y in range(dim)]
plt.clf()
fig, ax = plt.subplots(dim, dim, figsize=(10, 10))
cnt = 0
mat = np.zeros((dim, dim))
df = pd.DataFrame(mat)
for i, freei, j, freej in flat_iter:
free_param = set([
freei, freej
]) # construct a small-set out of the indexed keys 2. If both keys are
# are the same, this set will only contain one index
bs = set(
hof[0].dtc.attrs.keys()
) # construct a full set out of all of the keys available, including ones not indexed here.
diff = bs.difference(
free_param) # diff is simply the key that is not indexed.
# hc is the dictionary of parameters to be held constant
# if the plot is 1D then two parameters should be held constant.
hc = {}
for d in diff:
hc[d] = hof[0].dtc.attrs[d]
cpparams = {}
if i == j:
assert len(free_param) == len(hc) - 1
assert len(hc) == len(free_param) + 1
# zoom in on optima
cpparams['freei'] = (np.min(params[freei]), np.max(params[freei]))
gr = run_grid(10,
tests,
provided_keys=freei,
hold_constant=hc,
mp_in=params)
# make a psuedo test, that still depends on input Parametersself.
# each test evaluates a normal PDP.
fp = list(copy.copy(free_param))
ax[i, j] = plot_line(gr, ax[i, j], fp)
if i > j:
assert len(free_param) == len(hc) + 1
assert len(hc) == len(free_param) - 1
cpparams['freei'] = (np.min(params[freei]), np.max(params[freei]))
cpparams['freej'] = (np.min(params[freej]), np.max(params[freej]))
gr = run_grid(10,
tests,
provided_keys=list((freei, freej)),
hold_constant=hc,
mp_in=params)
fp = list(copy.copy(free_param))
ax[i, j] = plot_surface(gr, ax[i, j], fp, imshow=False)
if i < j:
free_param = list(copy.copy(list(free_param)))
if len(free_param) == 2:
ax[i, j] = plot_scatter(hof, ax[i, j], free_param)
# To Pandas:
k = 0
df.insert(i, j, k, free_param)
k = 1
df.insert(i, j, k, hc)
k = 2
df.insert(i, j, k, cpparams)
k = 3
df.insert(i, j, k, gr)
'''
where, i and j are indexs to the 3 by 3 (9 element) subplot matrix,
and `k`-dim-0 is the parameter(s) that were free to vary (this can be two free in the case for i<j,
or one free to vary for i==j).
`k`-dim-1, is the parameter(s) that were held constant.
`k`-dim-2 `cpparams` is a per parameter dictionary, whose values are tuples that mark the edges of (free)
parameter ranges. `k`-dim-3 is the the grid that results from varying those parameters
(the grid results can either be square (if len(free_param)==2), or a line (if len(free_param==1)).
'''
plt.savefig(str('cross_section_and_surfaces.png'))
return matrix, df
def grids(hof, tests, ranges, us, history):
'''
Obtain using the best candidate Gene (HOF, NU-tests, and expanded parameter ranges found via
exploring extreme edge cases of parameters
plot a error surfaces, and cross sections, about the optima in a 3by3 subplot matrix.
where, i and j are indexs to the 3 by 3 (9 element) subplot matrix,
and `k`-dim-0 is the parameter(s) that were free to vary (this can be two free in the case for i<j,
or one free to vary for i==j).
`k`-dim-1, is the parameter(s) that were held constant.
`k`-dim-2 `cpparams` is a per parameter dictionary, whose values are tuples that mark the edges of (free)
parameter ranges. `k`-dim-3 is the the grid that results from varying those parameters
(the grid results can either be square (if len(free_param)==2), or a line (if len(free_param==1)).
'''
#scores = hof[0].dtc.scores = OrderedDict(hof[0].dtc.scores)
hof[0].dtc.attrs = OrderedDict(hof[0].dtc.attrs)
attrs = hof[0].dtc.attrs
dim = len(hof[0].dtc.attrs.keys())
best_param_keys = hof[0].dtc.attrs.keys()
flat_iter = iter([(i, freei, j, freej)
for i, freei in enumerate(best_param_keys)
for j, freej in enumerate(best_param_keys)])
plt.clf()
fig0, ax0 = plt.subplots(dim, dim, figsize=(10, 10))
#fig1,ax1 = plt.subplots(dim,dim,figsize=(10,10))
cnt = 0
temp = []
loc_key = {}
for k, v in attrs.items():
loc_key[k] = attrs[k]
ranges[k] = (loc_key[k] - 1 * np.abs(ranges[k]),
loc_key[k] + 1 * np.abs(ranges[k]))
for i, freei, j, freej in flat_iter:
if i == j:
free_param = freei
else:
free_param = [freei, freej]
free_param_set = set(
free_param
) # construct a small-set out of the indexed keys 2. If both keys are
# are the same, this set will only contain one index
bs = set(
best_param_keys
) # construct a full set out of all of the keys available, including ones not indexed here.
diff = bs.difference(
free_param_set) # diff is simply the key that is not indexed.
# hc is the dictionary of parameters to be held constant
# if the plot is 1D then two parameters should be held constant.
hc = {}
for d in diff:
hc[d] = hof[0].dtc.attrs[d]
cpparams = {}
cpparams['freei'] = (np.min(ranges[freei]), np.max(ranges[freei]))
# make a psuedo test, that still depends on input Parametersself.
# each test evaluates a normal PDP.
fp = list(copy.copy(free_param))
#plot_line_ss(gr,ax,key,hof,free,constant)
if i == j:
gr = run_simple_grid(10, tests, ranges, freei, hold_constant=hc)
ax0[i, j] = plot_line_ss(gr, ax0[i, j], freei, hof, hc)
if i > j:
#assert len(free_param) == len(hc) + 1
#assert len(hc) == len(free_param) - 1
cpparams['freei'] = (np.min(ranges[freei]), np.max(ranges[freei]))
cpparams['freej'] = (np.min(ranges[freej]), np.max(ranges[freej]))
free_params = [freei, freej]
gr = run_simple_grid(10,
tests,
ranges,
free_params,
hold_constant=hc)
#gr = run_grid(10,tests,, hold_constant = hc, mp_in = params)
fp = list(copy.copy(free_param))
#ax0[i,j],img = plot_surface(gr,ax0[i,j],fp,hc,imshow=True)
ax0[i, j], img = plot_surface(gr, ax0[i, j], fp, hc, imshow=True)
#plt.colorbar(img, ax = ax0[i,j])
#ax1[i,j] = plot_surface(gr,ax1[i,j],fp,imshow=False)
if i < j:
free_param = list(copy.copy(list(free_param)))
#if len(free_param) == 2:
ax0[i, j] = plot_scatter(history, ax0[i, j], free_param, hc)
#ax0[i,j] = ps(fig0,ax1[i,j],freei,freej,history)
cpparams['freei'] = (np.min(ranges[freei]), np.max(ranges[freei]))
cpparams['freej'] = (np.min(ranges[freej]), np.max(ranges[freej]))
gr = hof
limits_used = (us[str(freei)], us[str(freej)])
scores = [g.dtc.get_ss() for g in gr]
params_ = [g.dtc.attrs for g in gr]
# To Pandas:
# https://stackoverflow.com/questions/28056171/how-to-build-and-fill-pandas-dataframe-from-for-loop#28058264
temp.append({
'i': i,
'j': j,
'free_param': free_param,
'hold_constant': hc,
'param_boundaries': cpparams,
'scores': scores,
'params': params_,
'ga_used': limits_used,
'grid': gr
})
#print(temp)
#intermediate = pd.DataFrame(temp)blah
with open('intermediate.p', 'wb') as f:
pickle.dump(temp, f)
#df = pd.DataFrame(temp)
plt.savefig(str('cross_section_and_surfaces.png'))
return temp
('TC_burst', (200, 1.6, -60, -50, 35, 0.01, 15, -60, 10, 6)),
('RTN', (40, 0.25, -65, -45, 0, 0.015, 10, -55, 50, 7)),
('RTN_burst', (40, 0.25, -65, -45, 0, 0.015, 10, -55, 50, 7))
])
import numpy as np
reduced_dict = OrderedDict([
(k, []) for k in ['C', 'k', 'vr', 'vt', 'vPeak', 'a', 'b', 'c', 'd']
])
#OrderedDict
for i, k in enumerate(reduced_dict.keys()):
for v in reduced2007.values():
reduced_dict[k].append(v[i])
explore_param = {k: (np.min(v), np.max(v)) for k, v in reduced_dict.items()}
opt_keys = [str('vr'), str('a'), str('b')]
nparams = len(opt_keys)
##
# find an optima copy and paste reverse search here.
##
#IB = mparams[param_dict['IB']]
RS = {}
IB = {}
TC = {}
CH = {}
RTN_burst = {}
cells = OrderedDict([