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if args.seed is None:
pattern = re.compile(r'_s(\d+)_')
m = pattern.search(os.path.basename(args.caffemodel))
if m:
seed = int(m.group(1))
else:
raise ValueError('Could not automatically determine seed')
else:
seed = args.seed
print('Seed:', seed)
scores = net.forward_all(data=x).values()[0].squeeze((2, 3))
yhat = scores.argmax(-1)
if args.output:
dd.io.save(args.output, dict(scores=scores, labels=y, name=name, seed=seed))
success = (yhat == y).mean()
error = 1 - success
print('Success: {:.2f}% / Error: {:.2f}%'.format(success * 100, error * 100))
# store results in this directory
name = '_'.join([mdl.name, cellname, expt, stim, datetime.now().strftime('%Y.%m.%d-%H.%M')])
base = f'../results/{name}'
os.makedirs(base, exist_ok=True)
# define model callbacks
cbs = [cb.ModelCheckpoint(os.path.join(base, 'weights-{epoch:03d}-{val_loss:.3f}.h5')),
cb.TensorBoard(log_dir=base, histogram_freq=1, batch_size=5000, write_grads=True),
cb.ReduceLROnPlateau(min_lr=0, factor=0.2, patience=10),
cb.CSVLogger(os.path.join(base, 'training.csv')),
cb.EarlyStopping(monitor='val_loss', patience=20)]
# train
history = mdl.fit(x=data.X, y=data.y, batch_size=bz, epochs=nb_epochs,
callbacks=cbs, validation_split=val_split, shuffle=True)
dd.io.save(os.path.join(base, 'history.h5'), history.history)
return history
Pez = mesh.getInterpolationMat(meshCore.gridCC, locType="Ez")
Pfx = mesh.getInterpolationMat(meshCore.gridCC, locType="Fx")
Pfy = mesh.getInterpolationMat(meshCore.gridCC, locType="Fy")
Pfz = mesh.getInterpolationMat(meshCore.gridCC, locType="Fz")
sigma_core = sigma[actinds]
def getEBJcore(src0):
B0 = np.r_[Pfx*f[src0, "b"], Pfy*f[src0, "b"], Pfz*f[src0, "b"]]
E0 = np.r_[Pex*f[src0, "e"], Pey*f[src0, "e"], Pez*f[src0, "e"]]
J0 = Utils.sdiag(np.r_[sigma_core, sigma_core, sigma_core]) * E0
return E0, B0, J0
E, B, J = getEBJcore(src)
tdem_is = { "E": E, "B": B, "J": J,
"sigma": sigma_core, "mesh": meshCore.serialize(), 'time':prb.times}
dd.io.save(fname, tdem_is)
dtypes = elem.dtypes.to_dict()
data_atts_separated[f"list_{i}_cols__{k}"] = cols
data_atts_separated[f"list_{i}_idx__{k}"] = idx
data_atts_separated[f"list_{i}_vals__{k}"] = vals
data_atts_separated[f"list_{i}_dtypes__{k}"] = dtypes
else:
raise TypeError(f"Value is list but list item is {type(elem)} not pd.DataFrame")
# Combine all attributes into a single dict and save with dd
model_atts = {}
model_atts['simple_atts'] = simple_atts
model_atts['data_atts'] = data_atts_separated
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=FutureWarning)
warnings.simplefilter("ignore", category=NaturalNameWarning)
dd.io.save(filepath, model_atts, compression=compression, **kwargs)
assert os.path.exists(filepath)
# Now deal with model object in R if needed
if model.model_obj is not None:
base.saveRDS(model.model_obj, f"{filename}.rds")
assert os.path.exists(f"{filename}.rds")
else:
raise IOError("filepath must end with .h5 or .hdf5")
'data' : self.data,
'analysis' : self.analysis,
'list_length' : self.list_length,
'n_lists' : self.n_lists,
'n_subjects' : self.n_subjects,
'position' : self.position,
'date_created' : self.date_created,
'meta' : self.meta
}
if fname[-4:]!='.fegg':
fname+='.fegg'
with warnings.catch_warnings():
warnings.simplefilter("ignore")
dd.io.save(fname, egg, compression=compression)
'reduce' : self.reduce,
'align' : self.align,
'normalize' : self.normalize,
'semantic' : self.semantic,
'corpus' : np.array(self.corpus) if isinstance(self.corpus, list) else self.corpus,
'kwargs' : self.kwargs,
'version' : self.version,
'dtype' : self.dtype
}
# if extension wasn't included, add it
if fname[-4:]!='.geo':
fname+='.geo'
# save
dd.io.save(fname, geo, compression=compression)
def create_weighted_db(X, y, weights, name='regression'):
X = X.reshape(-1, 3, 32, 32)
train_fn = os.path.join(DIR, '{}.h5'.format(name))
dd.io.save(train_fn, dict(data=X,
label=y.astype(np.float32),
sample_weight=weights), compress=False)
with open(os.path.join(DIR, '{}.txt'.format(name)), 'w') as f:
print(train_fn, file=f)
Pez = mesh.getInterpolationMat(meshCore.gridCC, locType="Ez")
Pfx = mesh.getInterpolationMat(meshCore.gridCC, locType="Fx")
Pfy = mesh.getInterpolationMat(meshCore.gridCC, locType="Fy")
Pfz = mesh.getInterpolationMat(meshCore.gridCC, locType="Fz")
sigma_core = sigma[actinds]
def getEBJcore(src0):
B0 = np.r_[Pfx*f[src0, "b"], Pfy*f[src0, "b"], Pfz*f[src0, "b"]]
E0 = np.r_[Pex*f[src0, "e"], Pey*f[src0, "e"], Pez*f[src0, "e"]]
J0 = Utils.sdiag(np.r_[sigma_core, sigma_core, sigma_core]) * E0
return E0, B0, J0
E, B, J = getEBJcore(src)
tdem_gs = { "E": E, "B": B, "J": J,
"sigma": sigma_core, "mesh": meshCore.serialize(), 'time':prb.times-t0, 'input_currents':input_currents}
dd.io.save(fname, tdem_gs)
def create_weighted_db(X, y, weights, name='boost'):
X = X.reshape(-1, 3, 32, 32)
train_fn = os.path.join(DIR, name + '.h5')
dd.io.save(train_fn, dict(data=X,
label=y.astype(np.float32),
sample_weight=weights), compress=False)
with open(os.path.join(DIR, name + '.txt'), 'w') as f:
print(train_fn, file=f)