def init_pop(dim, pop_size):
qNom = np.zeros(dim)
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
pop = pg.population(prob=optimizeRes(dim, out=outputFile))
pop.push_back(x=qNom, f=np.zeros(p_optimizeRes.get_nobj())) #[0:dim])
print(pop)
print(pop.problem.get_fevals())
pop.set_x(0, qNom)
print(pop)
for i in range(pop_size - 1):
pop.push_back(pop.random_decision_vector())
return pop
def main(pop_init=None):
# start timer
startTime = timeit.default_timer()
# initialize algorithm with hyperparameters
alg = pg.moead(gen=generations, neighbours=neighbors, seed=seed)
# there should be a way to run batch_fitness evaluations, haven't gotten it to work on NSCL
#b = pg.bfe()
#alg.set_bfe(b)
#alg.set_verbosity(1)
# initialize problem
p_optimizeRes = pg.problem(optimizeRes(magnet_dim, outputFile))
# relic from old evolutions, which launched all islands internally
# this can allow for interconnectivity between islands
# now each run of this script calls its own island
n_islands = 1
# if more than one island and want to exchange info need to define a topology to connect them
#top = pg.topology(pg.fully_connected(n_islands,1.0))
# when running 5 objectives, pop needed to be 70
pop_n = 70 #84
if p_optimizeRes.get_nobj() == 4:
# with 4 objs need pop=84
pop_n = 84
# check if we are using an input population or need to initialize one
pop_new = None
if (pop_init == None):
# randomly create a new population of size pop_n
pop_new = pg.population(p_optimizeRes, size=pop_n)
print("initialize pop")
else:
pop_new = pop_init
print("provided pop")
# create archipelago from algorithm (of a single island)
archi = pg.algorithm(alg)
# evolve archipelago
archi.evolve(pop_new)
# check total time
print('Running time (sec): %f' % (timeit.default_timer() - startTime))
# when I tried to use multiprocessing I needed this
#pg.mp_island.shutdown_pool()
#pg.mp_bfe.shutdown_pool()
return pop_new
def read_pop_df(filename, pop=None):
df = pd.read_hdf(filename)
max_val = 1e9
df = df.loc[(df['FP2_res'] < max_val) & (df['FP3_res'] < max_val) &
(df['MaxBeamWidth'] < max_val) &
(df['FP4_BeamSpot'] < max_val)]
df = df.reindex()
magnet_dim = len(df.columns) - optimized_params
# df = df.loc[(df['FP2_res'] < 1.0) & (df['FP2_e_xangle'] < 1.0) & (df['FP3_res'] < 1.0) & (df['FP3_e_xangle'] <1.0)]
# costs = df[['FP2_res','FP2_e_xangle','FP3_res','FP3_e_xangle']]
# costs = np.array(costs)
# pareto = is_pareto_efficient_simple(costs)
# df['pareto'] = pareto
# print(np.count_nonzero(pareto) )
# df = (df.loc[(df['pareto']==True)])
# df = df.sort_values(by='FP2_res',ignore_index=True)
# df["f0"] = df['f0'] * 1.0 / 4.419411469795324
# df['f1'] = df['f1'] * 1.0 / 2.7701491204695756
# print(magnet_dim)
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
if pop == None:
pop = pg.population(p_optimizeRes)
# df_2 = df.loc[(df["f0"] < 10) & (df["f1"] < 10) & (df["f2"] < 10) & (df["f3"] < 10)]
# df = df_2
nrow, ncol = df.shape
# print(df.index)
for i in df.index:
if i > 26000:
break
# print(i)
append = True
xs = []
for j in range(1, magnet_dim + 1):
xs.append(df["q" + str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(magnet_dim, ncol + 0):
# if j > 0:
# fs.append(df["f"+str(j)][i]/fNom[j])
# else:
# if df["f"+str(j)][i] >= 1.0:
# append=False
# if df["f"+str(j)][i] < 0 or np.isnan(df["f"+str(j)][i]):
# print(df["f"+str(j)][i], i)
fs.append(df.iloc[i, j])
if append:
pop.push_back(xs, f=fs)
# print(pop)
return pop
def read_pop(filename, pop=None):
df = pd.read_csv(filename,
names=[
"x0", "x1", "x2", "x3", "x4", "x5", "x6", "f0", "f1",
"f2", "f3"
])
magnet_dim = len(df.columns) - optimized_params
quads = []
for i in range(magnet_dim):
quads.append("x{}".format(i))
columns = quads
columns.append("f0")
columns.append("f1")
columns.append("f2")
columns.append("f3")
# df["f0"] = df['f0'] * 1.0 / 4.419411469795324
# df['f1'] = df['f1'] * 1.0 / 2.7701491204695756
# print(magnet_dim)
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
if pop == None:
pop = pg.population(p_optimizeRes)
# df_2 = df.loc[(df["f0"] < 10) & (df["f1"] < 10) & (df["f2"] < 10) & (df["f3"] < 10)]
# df = df_2
nrow, ncol = df.shape
# print(df)
for i in df.index:
append = True
xs = []
for j in range(magnet_dim):
xs.append(df["x" + str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(ncol - magnet_dim):
# if j > 0:
# fs.append(df["f"+str(j)][i]/fNom[j])
# else:
# if df["f"+str(j)][i] >= 1.0:
# append=False
if df["f" + str(j)][i] < 0 or np.isnan(df["f" + str(j)][i]):
print(df["f" + str(j)][i], i)
fs.append(df["f" + str(j)][i])
if append:
pop.push_back(xs, f=fs)
# print(pop)
return pop
def read_pop(filename):
df = pd.read_csv(filename)
p_optimizeRes = pg.problem(optimizeRes(magnet_dim, out=outputFile))
pop = pg.population(p_optimizeRes)
nrow, ncol = df.shape
print(df)
for i in range(nrow):
xs = []
for j in range(magnet_dim):
xs.append(df["x" + str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(ncol - magnet_dim):
fs.append(df["f" + str(j)][i])
pop.push_back(xs, f=fs)
return pop
def read_pop(filename, pop=None):
# df = pd.read_csv(filename,names=["x0","x1","x2","x3","x4","x5","x6","f0","f1","f2","f3"])
magnet_dim = len(pd.read_csv(filename).columns) - optimized_params
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
obj_dim = p_optimizeRes.get_nobj()
quads = []
for i in range(magnet_dim):
quads.append("x{}".format(i))
columns = quads
for i in range(obj_dim):
columns.append("f{}".format(i))
df = pd.read_csv(filename, names=columns)
# df["f0"] = df['f0'] * 1.0 / 4.419411469795324
# df['f1'] = df['f1'] * 1.0 / 2.7701491204695756
# print(magnet_dim)
if pop == None:
pop = pg.population(p_optimizeRes)
# df_2 = df.loc[(df["f0"] < 10) & (df["f1"] < 10) & (df["f2"] < 10) & (df["f3"] < 10)]
# df = df_2
nrow, ncol = df.shape
# print(df)
for i in df.index:
# if i in [0,102,76]:
# continue
# for i in range(nrow):
xs = []
for j in range(magnet_dim):
xs.append(df["x" + str(j)][i])
xs = np.asarray(xs)
fs = []
# print(ncol, magnet_dim)
for j in range(ncol - magnet_dim):
# if j > 0:
# fs.append(df["f"+str(j)][i]/fNom[j])
# else:
if df["f" + str(j)][i] < 0 or np.isnan(df["f" + str(j)][i]):
print(df["f" + str(j)][i], i)
df["f" + str(j)][i] = 1e10
fs.append(df["f" + str(j)][i])
if np.all(np.array(fs) < 1) == True or True:
pop.push_back(xs, f=fs)
# print(pop)
return pop
def read_pop_df(filename, pop=None):
df = pd.read_hdf(filename)
magnet_dim = 15
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
nobj = p_optimizeRes.get_nobj()
if pop == None:
pop = pg.population(p_optimizeRes)
nrow, ncol = df.shape
for i in df.index:
append=True
xs = []
for j in range(1,magnet_dim+1):
xs.append(df["q"+str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(magnet_dim,magnet_dim+nobj):
# if i == 0:
# print(df.iloc[i,magnet_dim:magnet_dim+p_optimizeRes.get_nobj()])
fs.append(df.iloc[i,j])
if append:
pop.push_back(xs,f=fs)
return pop, df
def read_pop(filename,pop=None):
# get magnet dimensions
magnet_dim = len(pd.read_csv(filename).columns)-optimized_params
# init problem for creating pop
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
obj_dim = p_optimizeRes.get_nobj()
quads = []
# construct columns to read from csv
for i in range(magnet_dim):
quads.append("x{}".format(i))
columns = quads
for i in range(obj_dim):
columns.append("f{}".format(i))
# read df from csv
df = pd.read_csv(filename,names=columns)
# initialize pop if none
if pop == None:
pop = pg.population(p_optimizeRes)
# construct pop from df
nrow, ncol = df.shape
for i in df.index:
xs = []
for j in range(magnet_dim):
xs.append(df["x"+str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(ncol-magnet_dim):
# if not a valid obj value throw out point
if df["f"+str(j)][i] < 0 or np.isnan(df["f"+str(j)][i]):
print("error: ", df["f"+str(j)][i], i)
df["f"+str(j)][i] = 1e10
fs.append(df["f"+str(j)][i])
# add point to population
pop.push_back(xs,f=fs)
# return population to main()
return pop
def plot_4d(popi,filename,df):
pop = None
for i_cluster in range(10):
df_i = df.loc[(df['kcluster'] == i_cluster)]
magnet_dim = 15
p_optimizeRes = pg.problem(optimizeRes(magnet_dim))
nobj = p_optimizeRes.get_nobj()
if pop == None:
pop = pg.population(p_optimizeRes)
nrow, ncol = df_i.shape
for i in df_i.index:
append=True
xs = []
for j in range(1,magnet_dim+1):
xs.append(df_i["q"+str(j)][i])
xs = np.asarray(xs)
fs = []
for j in range(magnet_dim,magnet_dim+nobj):
# if i == 0:
# print(df.iloc[i,magnet_dim:magnet_dim+p_optimizeRes.get_nobj()])
fs.append(df.iloc[i,j])
if append:
pop.push_back(xs,f=fs)
popi = pop
sort_param = 3
good_results=0
magnet_dim = len(popi.get_x()[0])
hv = pg.hypervolume(popi)
ref_point = np.zeros(optimized_params)+1e10
ndf, dl, dc, ndl = pg.fast_non_dominated_sorting(popi.get_f())
plot_x, plot_y = 0,0
fig, axs = plt.subplots(optimized_params-1,sharex=True)
fig.suptitle('Pareto Fronts of each parameter vs. BeamSpotSize at FP4')
axs[optimized_params-2].set_xlabel(fNames[sort_param])
reduced_ndf = []
first = True
# df_closest = df.loc[(df['kcluster'] == i_cluster)]
for j in range(0,optimized_params-1):
ndf_champ = []
axs[plot_y].axvline(x=fNom[0],linestyle="dashed",color="red")
axs[plot_y].axhline(y=1.0,linestyle="dashed",color="red")
for i in ndf[0]:
check_val=1e9
if np.all(np.array(popi.get_f()[i]) < check_val) == True:
good_results+=1
# print(filename[-6:-4], good_results, popi.get_f()[i])
ndf_champ.append(popi.get_f()[i])
reduced_ndf.append(i)
try:
pg.plot_non_dominated_fronts(ndf_champ,comp=[sort_param,j],axes=axs[plot_y])
# if j == 1:
# print(filename[-6:-4], len(ndf_champ))
except:
print(filename[-6:-4], "no better than nominal solutions")
return
if "closest" in df_i.columns:
df_closest = df_i.loc[df['closest']==True]
df_closest = df_closest.reset_index(drop=True)
# print(df_closest.iloc[:,15:19])
for i_closest in df_closest.index:
axs[plot_y].text(df_closest.iloc[:,18][i_closest],df_closest.iloc[:,15+j][i_closest],str(df_closest['kcluster'][0]+1),color='red')
axs[plot_y].set_ylabel(fNames[j])
axs[plot_y].set_yscale('log')
axs[plot_y].set_xscale('log')
plot_y += 1
fig.tight_layout()
fig.savefig(filename+"{}_paretos.png".format(i_cluster))
plt.cla()
fig2, axs2 = plt.subplots(4,4)
plot_x, plot_y = 0,0
reduced_qs = np.array(popi.get_x())[reduced_ndf]
ycolumns = []
for i in range(magnet_dim):
ycolumns.append('y{}'.format(i))
df_i = pd.DataFrame(reduced_qs, columns = ycolumns)
qNom = np.zeros(magnet_dim)
for i in range(magnet_dim):
if plot_x > 3:
plot_x, plot_y = 0, plot_y+1
axs2[plot_y,plot_x] = df_i['y{0}'.format(i)].plot.hist(ax=axs2[plot_y,plot_x],bins=100,range=(-2,2))
# axs2[plot_y,plot_x].axvline( x = qNom[i], ymin=0,ymax=20,color='red',linestyle='dashed')
# axs[plot_y,plot_x].axvline( x = max_y[i], ymin=0,ymax=20,color='green',linestyle='dashed')
axs2[plot_y,plot_x].axes.yaxis.set_visible(False)
# axs2[plot_y,plot_x].axes.set_yscale("log")
# axs2[plot_y,plot_x].axes.set_ylim(0.1,20)
xlower, xupper = popi.problem.get_bounds()
xlower, xupper = np.min(xlower), np.max(xupper)
axs2[plot_y,plot_x].axes.set_xlim(xlower,xupper)
axs2[plot_y,plot_x].set_title("q{0}".format(i+1))
y_min, y_max = axs2[plot_y,plot_x].get_ylim()
df_closest['yplot'] = pd.Series(df_closest['kcluster'][0]).apply(lambda x: x/(10)*(y_max-y_min)+y_min)
# print(df_closest.iloc[:,:15])
# if "closest" in df.columns:
for i_closest in df_closest.index:
axs2[plot_y,plot_x].text(df_closest["q{0}".format(i+1)][i_closest],df_closest['yplot'][i_closest],str(df_closest['kcluster'][0]+1),color='red')
plot_x += 1
fig2.delaxes(axs2[plot_y,plot_x])
fig2.tight_layout()
plt.savefig(filename + "{}_magnet_hists.png".format(i_cluster))
return