def load_experiments(args):
dataset_name = args.dataset_name
db = sql.db("postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s"
% {"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
logger.info("Getting dataset info for %s%s"
% (dataset_name, ", transposed" if args.transposed else ""))
data_path = serial.preprocess("${PYLEARN2_NI_PATH}/" + args.dataset_name)
if args.transposed:
logger.info("Data in transpose...")
mri = MRI.MRI_Transposed(dataset_name=args.dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
input_dim = mri.X.shape[1]
variance_map_file = path.join(data_path, "transposed_variance_map.npy")
else:
mask_file = path.join(data_path, "mask.npy")
mask = np.load(mask_file)
input_dim = (mask == 1).sum()
if input_dim % 2 == 1:
input_dim -= 1
mri = MRI.MRI_Standard(which_set="full",
dataset_name=args.dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
variance_map_file = path.join(data_path, "variance_map.npy")
mri_nifti.save_variance_map(mri, variance_map_file)
for items in nested_generator(layer_depth_generator("encoder.layer_depths",
xrange(4, 6), 5),
hidden_generator("encoder.nhid", 4),
float_generator("weight_decay.coeffs.z", 3, 0.1, 0.001, log_scale=True)):
# logger.info("Adding NICE experiment with hyperparameters %s" % (items, ))
state = DD()
experiment_hyperparams = nice_experiment.default_hyperparams(input_dim)
if args.transposed:
experiment_hyperparams["data_class"] = "MRI_Transposed"
if args.logistic:
experiment_hyperparams["prior"]["__builder__"] =\
"nice.pylearn2.models.nice.StandardLogistic"
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
entry[split_keys[-1]] = value
experiment_hyperparams["dataset_name"] = dataset_name
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
[tuple(v) if isinstance(v, list) else v for v in flatten(experiment_hyperparams).values()])))
user = path.expandvars("$USER")
save_path = serial.preprocess("/export/mialab/users/%s/pylearn2_outs/%d"
% (user, h))
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
sql.insert_job(
nice_experiment.experiment,
flatten(state),
db
)
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
db = sql.db(
"postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s" %
{
"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
logger.info("Getting dataset info for %s" % dataset_name)
data_path = serial.preprocess("${PYLEARN2_NI_PATH}/" + dataset_name)
mask_file = path.join(data_path, "mask.npy")
mask = np.load(mask_file)
input_dim = (mask == 1).sum()
if input_dim % 2 == 1:
input_dim -= 1
mri = MRI.MRI_Standard(which_set="full",
dataset_name=dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
variance_map_file = path.join(data_path, "variance_map.npy")
mri_nifti.save_variance_map(mri, variance_map_file)
for items in jg.nested_generator(
jg.hidden_generator("nhid1", 1),
jg.hidden_generator("nhid2", 1),
):
state = DD()
experiment_hyperparams = mlp_experiment.default_hyperparams(input_dim)
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
entry[split_keys[-1]] = value
experiment_hyperparams["dataset_name"] = dataset_name
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
flatten(experiment_hyperparams).values())))
user = path.expandvars("$USER")
save_path = serial.preprocess(
"/export/mialab/users/%s/pylearn2_outs/%d" % (user, h))
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
state.pid = 0
sql.insert_job(mlp_experiment.experiment, flatten(state), db)
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
# Load the database and table.
db = sql.db(
"postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s" %
{
"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
# Don't worry about this yet.
input_handler = InputHandler()
# For generating models, we use a special set of jobman generators, made
# for convenience.
for items in jg.nested_generator(
jg.float_generator("learning_rate",
3,
0.01,
0.0001,
log_scale=True),
jg.list_generator("nhid", [50, 100, 200, 300]),
):
logger.info("Adding RBM experiment across hyperparameters %s" %
(items, ))
state = DD()
# Load experiment hyperparams from experiment
experiment_hyperparams = experiment.default_hyperparams()
# Set them with values in our loop.
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
assert split_keys[-1] in entry, (
"Key not found in hyperparams: %s" % split_keys[-1])
entry[split_keys[-1]] = value
# Set the dataset name
experiment_hyperparams["dataset_name"] = dataset_name
# Get the input dim and variance map. Don't worry about variance maps right now,
# they aren't used here.
input_dim, variance_map_file = input_handler.get_input_params(
args, experiment_hyperparams)
logger.info("%s\n%s\n" % (input_dim, variance_map_file))
# Set the input dimensionality by the data
experiment_hyperparams["nvis"] = input_dim
# Set the minimum learning rate relative to the initial learning rate.
experiment_hyperparams[
"min_lr"] = experiment_hyperparams["learning_rate"] / 10
# Make a unique hash for experiments. Remember that lists, dicts, and other data
# types may not be hashable, so you may need to do some special processing. In
# this case we convert the lists to tuples.
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
[tuple(v) if isinstance(v, list)
else v
for v in flatten(experiment_hyperparams).values()])))
# Save path for the experiments. In this case we are sharing a directory in my
# export directory so IT can blame me.
save_path = serial.preprocess(
"/export/mialab/users/dhjelm/pylearn2_outs/rbm_demo/%d" % h)
# We save file params separately as they aren't model specific.
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
user = path.expandvars("$USER")
state.created_by = user
# Finally we add the experiment to the table.
sql.insert_job(experiment.experiment, flatten(state), db)
# A view can be used when querying the database using psql. May not be needed in future.
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
db = sql.db(
"postgres://%(user)s@%(host)s:"
"%(port)d/%(database)s?table=%(table)s" % {
"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
input_handler = InputHandler()
for items in jg.nested_generator(
jg.list_generator(
"encoder.layer_depths",
[[3, 5, 5, 5, 3], [5, 5, 5, 5, 5], [2, 4, 4, 2]]),
jg.list_generator("variance_normalize", [False, 2]),
jg.float_generator("weight_decay.coeff",
4,
0.1,
0.0001,
log_scale=True),
jg.list_generator("prior.__builder__", [
"nice.pylearn2.models.nice.StandardNormal",
"nice.pylearn2.models.nice.StandardLogistic"
])):
logger.info("Adding NICE experiment across hyperparameters %s" %
(items, ))
state = DD()
experiment_hyperparams = nice_experiment.default_hyperparams()
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
assert split_keys[-1] in entry,\
("Key not found in hyperparams: %s, "
"found: %s" % (split_keys[-1], entry.keys()))
entry[split_keys[-1]] = value
experiment_hyperparams["dataset_name"] = dataset_name
input_dim, variance_map_file = input_handler.get_input_params(
args, experiment_hyperparams)
logger.info("%s\n%s\n" % (input_dim, variance_map_file))
experiment_hyperparams["nvis"] = input_dim
experiment_hyperparams["encoder"]["nvis"] = input_dim
h = abs(hash(frozenset(
flatten(experiment_hyperparams).keys() +\
[tuple(v) if isinstance(v, list)
else v for v in flatten(experiment_hyperparams).values()])))
user = path.expandvars("$USER")
save_path = serial.preprocess(
"/export/mialab/users/%s/pylearn2_outs/%d" % (user, h))
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
sql.insert_job(nice_experiment.experiment, flatten(state), db)
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
db = sql.db(
"postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s" %
{
"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
logger.info("Getting dataset info for %s%s" %
(dataset_name, ", transposed" if args.transposed else ""))
data_path = serial.preprocess("${PYLEARN2_NI_PATH}/" + args.dataset_name)
if args.transposed:
logger.info("Data in transpose...")
mri = MRI.MRI_Transposed(dataset_name=args.dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
input_dim = mri.X.shape[1]
variance_map_file = path.join(data_path, "transposed_variance_map.npy")
else:
mask_file = path.join(data_path, "mask.npy")
mask = np.load(mask_file)
input_dim = (mask == 1).sum()
if input_dim % 2 == 1:
input_dim -= 1
mri = MRI.MRI_Standard(which_set="full",
dataset_name=args.dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
variance_map_file = path.join(data_path, "variance_map.npy")
mri_nifti.save_variance_map(mri, variance_map_file)
for items in nested_generator(
layer_depth_generator("encoder.layer_depths", xrange(4, 6), 5),
hidden_generator("encoder.nhid", 4),
float_generator("weight_decay.coeffs.z",
3,
0.1,
0.001,
log_scale=True)):
# logger.info("Adding NICE experiment with hyperparameters %s" % (items, ))
state = DD()
experiment_hyperparams = nice_experiment.default_hyperparams(input_dim)
if args.transposed:
experiment_hyperparams["data_class"] = "MRI_Transposed"
if args.logistic:
experiment_hyperparams["prior"]["__builder__"] =\
"nice.pylearn2.models.nice.StandardLogistic"
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
entry[split_keys[-1]] = value
experiment_hyperparams["dataset_name"] = dataset_name
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
[tuple(v) if isinstance(v, list) else v for v in flatten(experiment_hyperparams).values()])))
user = path.expandvars("$USER")
save_path = serial.preprocess(
"/export/mialab/users/%s/pylearn2_outs/%d" % (user, h))
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
sql.insert_job(nice_experiment.experiment, flatten(state), db)
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
db = sql.db("postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s"
% {"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
logger.info("Getting dataset info for %s" % dataset_name)
data_path = serial.preprocess("${PYLEARN2_NI_PATH}/" + dataset_name)
mask_file = path.join(data_path, "mask.npy")
mask = np.load(mask_file)
input_dim = (mask == 1).sum()
if input_dim % 2 == 1:
input_dim -= 1
mri = MRI.MRI_Standard(which_set="full",
dataset_name=dataset_name,
unit_normalize=True,
even_input=True,
apply_mask=True)
variance_map_file = path.join(data_path, "variance_map.npy")
mri_nifti.save_variance_map(mri, variance_map_file)
for items in jg.nested_generator(jg.hidden_generator("nhid1", 1),
jg.hidden_generator("nhid2", 1),
):
state = DD()
experiment_hyperparams = mlp_experiment.default_hyperparams(input_dim)
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
entry[split_keys[-1]] = value
experiment_hyperparams["dataset_name"] = dataset_name
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
flatten(experiment_hyperparams).values())))
user = path.expandvars("$USER")
save_path = serial.preprocess("/export/mialab/users/%s/pylearn2_outs/%d"
% (user, h))
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
state.pid = 0
sql.insert_job(
mlp_experiment.experiment,
flatten(state),
db
)
db.createView("%s_view" % args.table)
def load_experiments(args):
dataset_name = args.dataset_name
# Load the database and table.
db = sql.db("postgres://%(user)s@%(host)s:%(port)d/%(database)s?table=%(table)s"
% {"user": args.user,
"host": args.host,
"port": args.port,
"database": args.database,
"table": args.table,
})
# Don't worry about this yet.
input_handler = InputHandler()
# For generating models, we use a special set of jobman generators, made
# for convenience.
for items in jg.nested_generator(
jg.float_generator("learning_rate", 3, 0.01, 0.0001, log_scale=True),
jg.list_generator("nhid", [50, 100, 200, 300]),
):
logger.info("Adding RBM experiment across hyperparameters %s" % (items, ))
state = DD()
# Load experiment hyperparams from experiment
experiment_hyperparams = experiment.default_hyperparams()
# Set them with values in our loop.
for key, value in items:
split_keys = key.split(".")
entry = experiment_hyperparams
for k in split_keys[:-1]:
entry = entry[k]
assert split_keys[-1] in entry, ("Key not found in hyperparams: %s"
% split_keys[-1])
entry[split_keys[-1]] = value
# Set the dataset name
experiment_hyperparams["dataset_name"] = dataset_name
# Get the input dim and variance map. Don't worry about variance maps right now,
# they aren't used here.
input_dim, variance_map_file = input_handler.get_input_params(args,
experiment_hyperparams)
logger.info("%s\n%s\n" % (input_dim, variance_map_file))
# Set the input dimensionality by the data
experiment_hyperparams["nvis"] = input_dim
# Set the minimum learning rate relative to the initial learning rate.
experiment_hyperparams["min_lr"] = experiment_hyperparams["learning_rate"] / 10
# Make a unique hash for experiments. Remember that lists, dicts, and other data
# types may not be hashable, so you may need to do some special processing. In
# this case we convert the lists to tuples.
h = abs(hash(frozenset(flatten(experiment_hyperparams).keys() +\
[tuple(v) if isinstance(v, list)
else v
for v in flatten(experiment_hyperparams).values()])))
# Save path for the experiments. In this case we are sharing a directory in my
# export directory so IT can blame me.
save_path = serial.preprocess("/export/mialab/users/dhjelm/pylearn2_outs/rbm_demo/%d"
% h)
# We save file params separately as they aren't model specific.
file_params = {
"save_path": save_path,
"variance_map_file": variance_map_file,
}
state.file_parameters = file_params
state.hyper_parameters = experiment_hyperparams
user = path.expandvars("$USER")
state.created_by = user
# Finally we add the experiment to the table.
sql.insert_job(
experiment.experiment,
flatten(state),
db
)
# A view can be used when querying the database using psql. May not be needed in future.
db.createView("%s_view" % args.table)
