def run(patch_size,n_batch,pca_frac,overcomplete,learning_rate,final_learning_rate,n_grad_step,loss_type,n_gauss_dim,n_lat_samp,seed,param_save_freq,log_freq,sigma,s1,s2,S,device,PCA_truncation,dataset):
os.environ["CUDA_VISIBLE_DEVICES"]=str(device) #
np.random.seed(seed) # Set the RNG seed to ensure randomness
dirname = util.get_directory(direc="./model_output/",tag = loss_type + "_{}".format(n_gauss_dim))
params = {
"dataset":dataset,
"patch_size":patch_size,
"n_batch":n_batch,
"pca_frac":pca_frac,
"overcomplete":overcomplete,
"learning_rate":np.float32(learning_rate),
"final_learning_rate":np.float32(final_learning_rate),
"pca_truncation":PCA_truncation,
"n_grad_step":n_grad_step,
"loss_type":loss_type,
"n_gauss_dim":n_gauss_dim,
"n_lat_samp":n_lat_samp,
"sigma":np.float32(sigma),
"param_save_freq":param_save_freq,
"log_freq":log_freq,
"s1":np.float32(s1),
"s2":np.float32(s2),
"S":np.float32(S)
}
util.dump_file(dirname +"/model_params",params)
LOG = log.log(dirname + "/logfile.csv")
netpar = prepare_network(params) #
var = netpar["variance"] #
loss_exp = netpar["loss_exp"] #
recon_err = netpar["recon_err"] #
images = netpar["images"] #
data = netpar["data"] #
varif = netpar["vardat"] #
#get factor to multiply LR by:
if final_learning_rate < learning_rate:
LR_factor = np.float32(np.exp(-np.log(learning_rate/final_learning_rate)/n_grad_step))
else:
print("Final LR must be lower than initial LR! Overriding with LR_factor = 1")
LR_factor = np.float32(1)
LR = tf.Variable(np.float32(learning_rate),trainable = False)#
adam = tf.train.AdamOptimizer(learning_rate = LR) # Set up the Adam optimization
train = adam.minimize(loss_exp) # Run training
update_LR = tf.assign(LR,LR*LR_factor)
run_training_loop(data,varif,images,netpar["mean"],n_batch,train,loss_exp,recon_err,LOG,dirname,log_freq,n_grad_step,param_save_freq,update_LR)
def run(patch_size, n_batch, pca_frac, overcomplete, learning_rate,
n_grad_step, loss_type, n_gauss_dim, n_lat_samp, seed, param_save_freq,
log_freq, sigma, s1, s2, S, device, PCA_truncation, dataset):
os.environ["CUDA_VISIBLE_DEVICES"] = str(device)
np.random.seed(seed)
dirname = util.get_directory(direc="./model_output/",
tag=loss_type + "_{}".format(n_gauss_dim))
params = {
"dataset": dataset,
"patch_size": patch_size,
"n_batch": n_batch,
"pca_frac": pca_frac,
"overcomplete": overcomplete,
"learning_rate": np.float32(learning_rate),
"pca_truncation": PCA_truncation,
"n_grad_step": n_grad_step,
"loss_type": loss_type,
"n_gauss_dim": n_gauss_dim,
"n_lat_samp": n_lat_samp,
"sigma": np.float32(sigma),
"param_save_freq": param_save_freq,
"log_freq": log_freq,
"s1": np.float32(s1),
"s2": np.float32(s2),
"S": np.float32(S)
}
util.dump_file(dirname + "/model_params", params)
LOG = log.log(dirname + "/logfile.csv")
netpar = prepare_network(params)
var = netpar["variance"]
loss_exp = netpar["loss_exp"]
recon_err = netpar["recon_err"]
images = netpar["images"]
data = netpar["data"]
varif = netpar["vardat"]
LR = tf.Variable(np.float32(learning_rate), trainable=False)
adam = tf.train.AdamOptimizer(learning_rate=LR)
train = adam.minimize(loss_exp)
run_training_loop(data, varif, images, n_batch, train, loss_exp, recon_err,
LOG, dirname, log_freq, n_grad_step, param_save_freq)
def get_GSM_data(param):
nang = param["nori"]
scale = param["scale"]
fdist = param["fdist"]
fname = "GSM_{}_{}_{}".format(scale, nang, fdist)
imlist = glob.glob("/home/gbarello/data/BSDS300/images/*.jpg")
Clist = []
try:
FF = utils.load_file("/home/gbarello/data/datasets/GSM_filters/" +
fname)
LOG.log("Using pre-saved filters")
except:
LOG.log("Measuring Filters")
for i in imlist:
Clist.append(proc.get_phased_filter_samples(i, nang, scale, fdist))
LOG.log(i + "\t{}".format(len(Clist[-1])))
utils.dump_file(Clist,
"/home/gbarello/data/datasets/GSM_filters/" + fname)
#we want to sample from each image equally, so we find the list with the fewest entries
mlen = min([len(c) for c in Clist])
#randomise the list and cocnatenate them all into one list
Clist = np.array([c[np.random.choice(range(len(c)), mlen)] for c in Clist])
Clist = np.array([k for c in Clist for k in c])
fac = np.array([IQR(Clist[:, :, :, 0]), IQR(Clist[:, :, :, 1])])
Clist = Clist / np.array([[fac]])
np.random.shuffle(Clist)
return Clist, fac
print("Min : {}".format(np.min(np.reshape(DATA, [-1]))))
print("IQR : {}".format(IQR(np.reshape(DATA, [-1]))))
np.random.shuffle(DATA)
#run the fit
C, Q, F, P, LOUT = TRAIN.fit_general_MGSM(DATA,
segmentation,
EMreps=args["em_steps"],
batchsize=args["minibatch_size"],
lr=args["learning_rate"],
ngradstep=args["n_grad_steps"],
buff=args["stochastic_buffer"],
fq_shared=args["fq_shared"],
f_ID=args["f_ID"])
#once it is complete, make the directory and save the data
direc = utils.get_directory(direc="./model_files/", tag="model_file")
np.savetxt(direc + "/fac.csv", fac)
np.savetxt(direc + "/train_log.csv", LOUT)
utils.save_dict(direc + "/parameters", args)
utils.dump_file(direc + "/paths.pkl", paths)
utils.dump_file(direc + "/segs.pkl", segmentation)
utils.dump_file(direc + "/kernels.pkl", kernels)
utils.dump_file(direc + "/C.pkl", C)
utils.dump_file(direc + "/Q.pkl", Q)
utils.dump_file(direc + "/F.pkl", F)
utils.dump_file(direc + "/P.pkl", P)
def run_training_loop(data,vdata,input_tensor,pos_mean,batch_size,train_op,loss_op,recerr_op,log,dirname,log_freq,n_grad_step,save_freq,update_LR):
#
def var_loss(session,vdat,nbatch = 10):
# SUB-FUNCTION TO CALCULATE THE LOSS OF THE VAE
D = split_by_batches(vdat,batch_size,shuffle = False) # Shuffel and partition data into batches
loss = 0 # Initialize the loss to zero
rerr = 0 # Initialize the reconstruction loss to zero
nb = 0 # Initialize a counter over the number of batches
means = [] # Initialize mean storage array to an empty array
for d in D: # Loop through the different batches
nb += 1 # Update counter
l,r,m = session.run([loss_op,recerr_op,pos_mean],{input_tensor:d}) # TENSORFLOW: RUN A SESSION??
loss += l # Update the loss function
rerr += r # Update the reconstruction error
means.append(m) # Append the mean to the mean storage array
if nb == nbatch: # Check if passed the number of batches
break # ... if so, BREAK
loss /= nbatch # Normalize the loss to the number of batches
rerr /= nbatch # Normalize the reconstruction error to the number of batches
return loss,rerr,np.concatenate(means,axis = 0) # Return the loss the reconstruction error
init = tf.global_variables_initializer() #
config = tf.ConfigProto() # Initialize the tensorflow session configuration
config.gpu_options.allow_growth = True # Allow for memory growth
sess = tf.Session(config=config) # Start a tensorflow session
K.setsession(sess)
sess.run(init) # run the session
nloss = 0 # Initailize a loss
t1 = time.time() # Record start time
av_time = -1 #
efrac = .9 #
log.log(["grad_step","loss","recloss","var_loss","var_rec","learning_rate","time_rem"],PRINT = True)
t_loss_temp = [] #
t_rec_temp = [] #
lrflag = True #
saver = tf.train.Saver(max_to_keep = 1000) #
for grad_step in range(n_grad_step + 1): #
batch = data[np.random.choice(np.arange(len(data)),batch_size)] # Get a batch of data
_,loss,recloss,newLR = sess.run([train_op,loss_op,recerr_op,update_LR],{input_tensor:batch}) # Run a session to get the loss/reconstruction error
t_loss_temp.append(loss) # Append loss to the ????
t_rec_temp.append(recloss) # Append reconstruction error to the ?????
if grad_step % log_freq == 0:
if grad_step == 0:
av_time = -1
elif grad_step != 0 and av_time < 0:
av_time = (time.time() - t1)
else:
av_time = efrac*av_time + (1. - efrac)*(time.time() - t1)
t1 = time.time() #
trem = av_time*((n_grad_step)+1-grad_step) #
trem = trem / log_freq / 60. / 60. #
loss = np.mean(t_loss_temp) #
recloss = np.mean(t_rec_temp) #
vloss,vrec,means = var_loss(sess,vdata) #
log.log([grad_step,loss,recloss,vloss,vrec,newLR,trem],PRINT = True) #
t_loss_temp = [] #
t_rec_temp = [] #
if grad_step % save_freq == 0: #
util.dump_file(dirname + "/training_means_{}.pkl".format(grad_step),means)
saver.save(sess,dirname + "/saved_params/saved_model_{}".format(str(grad_step))) #
saver.save(sess,dirname + "/saved_params/saved_model_{}".format("final")) #
sess.close() #
def run_training_loop(data, vdata, input_tensor, pos_mean, batch_size,
train_op, loss_op, recerr_op, log, dirname, log_freq,
n_grad_step, save_freq, update_LR):
def var_loss(session, vdat, nbatch=10):
D = split_by_batches(vdat, batch_size, shuffle=False)
loss = 0
rerr = 0
nb = 0
means = []
for d in D:
nb += 1
l, r, m = session.run([loss_op, recerr_op, pos_mean],
{input_tensor: d})
loss += l
rerr += r
means.append(m)
if nb == nbatch:
break
loss /= nbatch
rerr /= nbatch
return loss, rerr, np.concatenate(means, axis=0)
init = tf.global_variables_initializer()
sess = tf.Session()
sess.run(init)
nloss = 0
t1 = time.time()
av_time = -1
efrac = .9
log.log([
"grad_step", "loss", "recloss", "var_loss", "var_rec", "learning_rate",
"time_rem"
],
PRINT=True)
t_loss_temp = []
t_rec_temp = []
lrflag = True
saver = tf.train.Saver(max_to_keep=1000)
for grad_step in range(n_grad_step + 1):
batch = data[np.random.choice(np.arange(len(data)), batch_size)]
_, loss, recloss, newLR = sess.run(
[train_op, loss_op, recerr_op, update_LR],
{input_tensor: batch
}) # Run a session to get the loss/reconstruction error
t_loss_temp.append(loss)
t_rec_temp.append(recloss)
if grad_step % log_freq == 0:
if grad_step == 0:
av_time = -1
elif grad_step != 0 and av_time < 0:
av_time = (time.time() - t1)
else:
av_time = efrac * av_time + (1. - efrac) * (time.time() - t1)
t1 = time.time()
trem = av_time * ((n_grad_step) + 1 - grad_step)
trem = trem / log_freq / 60. / 60.
loss = np.mean(t_loss_temp)
recloss = np.mean(t_rec_temp)
vloss, vrec, means = var_loss(sess, vdata)
log.log([grad_step, loss, recloss, vloss, vrec, newLR, trem],
PRINT=True) #
t_loss_temp = []
t_rec_temp = []
if grad_step % save_freq == 0:
util.dump_file(
dirname + "/training_means_{}.pkl".format(grad_step), means)
saver.save(
sess, dirname +
"/saved_params/saved_model_{}".format(str(grad_step)))
saver.save(sess, dirname + "/saved_params/saved_model_{}".format("final"))
sess.close()
def run():
def c2(c):
return np.array([[1., c], [c, 1.]])
def cov(n, w, dr=0):
distance = np.array([[((i - j + (n / 2.)) % n) - n / 2.
for i in range(n)] for j in range(n)])
gauss = np.exp(-(distance**2) / (2. * w * w)) - dr
out = np.dot(gauss, gauss)
return out / out[0, 0]
def inp(n, w, c1, c2, i):
stim1 = np.array([((j + (n / 2.)) % n) - (n / 2.) for j in range(n)])
stim2 = np.array([(((j - (i % n)) + (n / 2.)) % n) - (n / 2.)
for j in range(n)])
gauss1 = np.exp(-(stim1**2) / (2. * w * w))
gauss2 = np.exp(-(stim2**2) / (2. * w * w))
return c1 * gauss1 + c2 * gauss2
LO = []
HI = []
nnLO = []
nnHI = []
ip = np.array([[1, 0], [0, 1], [1, 1]])
for c in np.linspace(-.9, .9, 20):
print(c)
cov = c2(c)
nc = np.identity(2) * (1 + c)
sHI = GSM.gexp(0, 20 * ip, cov, nc * (2 * 2), precom=False)
sLO = GSM.gexp(0, ip, cov, nc * (2 * 2), precom=False)
snnLO = GSM.gnn(ip, cov)[:, 0]
snnHI = GSM.gnn(20 * ip, cov)[:, 0]
HI.append(sHI[2] / (sHI[0]))
LO.append(sLO[2] / (sLO[0]))
nnHI.append(snnHI[2] / (snnHI[0]))
nnLO.append(snnLO[2] / (snnLO[0]))
HI = np.array(HI)
LO = np.array(LO)
nnHI = np.array(nnHI)
nnLO = np.array(nnLO)
import utilities as utils
utils.dump_file("./inference/2Dmodel_stuff.pkl", [HI, LO, nnHI, nnLO])
exit()
plt.plot(HI[:, 0], [1 for x in HI], 'k--', linewidth=1)
plt.plot(HI[:, 0], HI[:, 1], 'k')
plt.plot(nnHI[:, 0], nnHI[:, 1], 'k--')
plt.plot(LO[:, 0], LO[:, 1], 'r')
plt.plot(nnLO[:, 0], nnLO[:, 1], 'r--')
plt.xlabel("Correlation")
plt.ylabel("Modulation Ratio")
plt.xlim(-1, 1)
plt.ylim(0, 2)
plt.xticks([-.5, 0, .5])
plt.tight_layout()
plt.savefig("./2DAIparam.pdf")
print("done with AI")
#what it is that we want to do here? We want to look at COS
con = 20 * np.logspace(-2, 0, 50)
NN = 2
WW = np.array([.15])
out1 = []
out2 = []
nnout1 = []
nnout2 = []
out12 = []
out22 = []
nnout12 = []
nnout22 = []
NCOV = np.identity(2)
k = .75
I1 = np.array([[c1, c1 / 10] for c1 in con])
I2 = np.array([[c1 + con[-1] / 10, con[-1] + c1 / 10] for c1 in con])
I12 = np.array([[c1, 0] for c1 in con])
I22 = np.array([[c1, con[-1]] for c1 in con])
print(I1.shape)
print(I2.shape)
CC = c2(.6)
NCOV = np.identity(2)
out1 = GSM.gexp(0, I1, CC, NCOV / (k * k), precom=False)
out2 = GSM.gexp(0, I2, CC, NCOV / (k * k), precom=False)
nnout1 = GSM.gnn(I1, CC).T
nnout2 = GSM.gnn(I2, CC).T
out12 = GSM.gexp(0, I12, CC, NCOV / (k * k), precom=False)
out22 = GSM.gexp(0, I22, CC, NCOV / (k * k), precom=False)
nnout12 = GSM.gnn(I12, CC).T
nnout22 = GSM.gnn(I22, CC).T
print(nnout2)
plt.figure()
plt.plot(con / con[-1], out1, 'r')
plt.plot(con / con[-1], out2, 'k')
plt.plot(con / con[-1], nnout1[0], 'r--')
plt.plot(con / con[-1], nnout2[0], 'k--')
plt.xlabel("contrast")
plt.ylabel("Respose")
# plt.yscale("log")
plt.xscale("log")
plt.tight_layout()
plt.savefig("./2Dssfig_0.pdf")
plt.figure()
plt.plot(con / con[-1], out12, 'r')
plt.plot(con / con[-1], out22, 'k')
plt.plot(con / con[-1], nnout12[0], 'r--')
plt.plot(con / con[-1], nnout22[0], 'k--')
plt.xlabel("contrast")
plt.ylabel("Respose")
# plt.yscale("log")
plt.xscale("log")
plt.tight_layout()
plt.savefig("./2Dssfig_1.pdf")
+
test.s_GRATC(args["con"],a + args["aux_angle"]*np.pi,k,r,T,surr = 0., A = A,offset = 0)]
if args["aux_scale"] < 0:
args["aux_scale"] = .3 * fullsize / (2 * pars["wavelengths"][0] * pars["filter_distance"])
grats = [[f(o,0,k,k*pars["filter_distance"]*args["aux_scale"],fullsize) for o in np.logspace(-2,0,args["npnt"]) for f in LF] for k in pars["wavelengths"]]
elif args["type"] == "test":
grats = [[stim.make_grating(o,0,k,fullsize/2,fullsize, A = A) for o in [.5]] for k in pars["wavelengths"][:1]]
elif args["type"] == "MI":
import att_MGSM_responses as aresp
RES,VRES = aresp.mutual_information_data(data,args["dt"])
utils.dump_file(direc + "/MI_responses_{}.pkl".format(args["dt"]),RES)
utils.dump_file(direc + "/MI_responses_variance_{}.pkl".format(args["dt"]),VRES)
exit()
elif args["type"] == "on_off":
import att_MGSM_responses as aresp
dt = .5
RES = aresp.on_off_response(data,args["snr"],dt,10)
utils.dump_file(direc + "/on_off_responses_{}_{}.pkl".format(args["snr"],dt),RES)
exit()
elif args["type"] == "nat_MI":
import att_MGSM_responses as aresp
RES = aresp.mutual_information_data(data,args["snr"],use_grat = False)
ax.plot(cc, [1 for k in range(len(cc))], 'k--')
plt.xlabel("Contrast")
plt.ylabel("A.I.")
plt.tight_layout()
fig.savefig("./paramfig_NC.pdf")
if __name__ == "__main__":
import utilities as utils
import time
out = []
NRUN = 1
for k in range(NRUN):
print(k)
t1 = time.time()
res = run_WDIFF_plots()
t2 = time.time()
if k > 0:
print("Time Left: {} minutes".format(
((t2 - t1) * (NRUN - k)) / 60))
out.append(res)
utils.dump_file("./inference/TAstim_TA_param_model_stuff.pkl", out)
# run_k()
#run_cov()
def export(self, loc):
util.dump_file(loc, self)