def run(config, num_checkpoint, epoch_end, output_filename):
task = get_task(config)
preprocess_opt = task.get_preprocess_opt()
dataloader = get_dataloader(config, 'train',
get_transform(config, 'dev', **preprocess_opt))
model = task.get_model()
checkpoints = get_checkpoints(config, num_checkpoint, epoch_end)
print('checkpoints:')
print('\n'.join(checkpoints))
utils.checkpoint.load_checkpoint(model, None, checkpoints[0])
for i, checkpoint in enumerate(checkpoints[1:]):
model2 = get_task(config).get_model()
last_epoch, _ = utils.checkpoint.load_checkpoint(
model2, None, checkpoint)
swa.moving_average(model, model2, 1. / (i + 2))
with torch.no_grad():
swa.bn_update(dataloader, model)
output_name = '{}.{}.{:03d}'.format(output_filename, num_checkpoint,
last_epoch)
print('save {}'.format(output_name))
utils.checkpoint.save_checkpoint(
config,
model,
None,
0,
0,
name=output_name,
weights_dict={'state_dict': model.state_dict()})
def setup_graph(args, graph, x_region, y_region, region, source=None, gpu=None, do_output=True,
index=0, make_reader=True):
backproject = get_task('general-backproject', processing_node=gpu)
if do_output:
if args.dry_run:
sink = get_task('null', processing_node=gpu, download=True)
else:
sink = get_writer(args)
sink.props.filename = '{}-{:>03}-%04i.tif'.format(args.output, index)
backproject.props.parameter = args.z_parameter
if args.burst:
backproject.props.burst = args.burst
backproject.props.z = args.z
backproject.props.region = region
backproject.props.x_region = x_region
backproject.props.y_region = y_region
backproject.props.center_position_x = (args.center_position_x or [args.width / 2.])
backproject.props.center_position_z = (args.center_position_z or [args.height / 2.])
backproject.props.source_position_x = args.source_position_x
backproject.props.source_position_y = args.source_position_y
backproject.props.source_position_z = args.source_position_z
backproject.props.detector_position_x = args.detector_position_x
backproject.props.detector_position_y = args.detector_position_y
backproject.props.detector_position_z = args.detector_position_z
backproject.props.detector_angle_x = args.detector_angle_x
backproject.props.detector_angle_y = args.detector_angle_y
backproject.props.detector_angle_z = args.detector_angle_z
backproject.props.axis_angle_x = args.axis_angle_x
backproject.props.axis_angle_y = args.axis_angle_y
backproject.props.axis_angle_z = args.axis_angle_z
backproject.props.volume_angle_x = args.volume_angle_x
backproject.props.volume_angle_y = args.volume_angle_y
backproject.props.volume_angle_z = args.volume_angle_z
backproject.props.num_projections = args.number
backproject.props.compute_type = args.compute_type
backproject.props.result_type = args.result_type
backproject.props.store_type = args.store_type
backproject.props.overall_angle = args.overall_angle
backproject.props.addressing_mode = args.genreco_padding_mode
backproject.props.gray_map_min = args.slice_gray_map[0]
backproject.props.gray_map_max = args.slice_gray_map[1]
source = create_preprocessing_pipeline(args, graph, source=source,
processing_node=gpu,
cone_beam_weight=not args.disable_cone_beam_weight,
make_reader=make_reader)
if source:
graph.connect_nodes(source, backproject)
else:
source = backproject
if do_output:
graph.connect_nodes(backproject, sink)
last = sink
else:
last = backproject
return (source, last)
def test_update_task():
task_id = tasks.save_task({"description": "before update", "status": "1"})
task = tasks.get_task(task_id)
assert task['description'] == "before update"
tasks.update_task(task_id, "after update")
task = tasks.get_task(task_id)
assert task['description'] == "after update"
def export_backup_status():
exports = dbstat.query('select * from stats where TYPE="EXPORT" and backup_start>="%s"' % mindate)
error = ""
finish=not runnings_backups()
if get_task() != None and finish:
status = get_task().get()
if status != "ok":
error = "Export failing with error: "+status
return jsonify(data=exports,finish=finish,error=error)
def _setup_task_data(self, task_enum, mols):
"""Setup target labels and attributions."""
task = att_tasks.get_task(task_enum)
if task_enum in TASKS_SKIP_DATA_LOAD:
proxy_task = att_tasks.get_task(att_tasks.Task.benzene)
y_true = np.zeros((len(mols), task.n_outputs))
y_true[:, 0] = 1.0
att_true = proxy_task.get_true_attributions(mols)
else:
y_true = task.get_true_predictions(mols)
att_true = task.get_true_attributions(mols)
return task, y_true, att_true
def export_backup_status():
exports = dbstat.query(
'select * from stats where TYPE="EXPORT" and backup_start>="%s"' %
mindate)
error = ""
finish = not runnings_backups()
if get_task() != None and finish:
status = get_task().get()
if status != "ok":
error = "Export failing with error: " + status
return jsonify(data=exports, finish=finish, error=error)
def run(config):
train_dir = config.train.dir
task = get_task(config)
optimizer = get_optimizer(config, task.get_model().parameters())
checkpoint = utils.checkpoint.get_initial_checkpoint(config)
if checkpoint is not None:
last_epoch, step = utils.checkpoint.load_checkpoint(
task.get_model(), optimizer, checkpoint)
else:
last_epoch, step = -1, -1
print('from checkpoint: {} last epoch:{}'.format(checkpoint, last_epoch))
scheduler = get_scheduler(config, optimizer, last_epoch)
preprocess_opt = task.get_preprocess_opt()
dataloaders = {
split: get_dataloader(config, split,
get_transform(config, split, **preprocess_opt))
for split in ['train', 'dev']
}
writer = SummaryWriter(config.train.dir)
train(config, task, dataloaders, optimizer, scheduler, writer,
last_epoch + 1)
def test_update():
"""
test updating a record
"""
tasks.add_task(datetime.date(2020, 4, 1), "Wake up")
tasks.edit_task(datetime.date(2020, 4, 1), 1, "Make coffee")
assert tasks.get_task(datetime.date(2020, 4, 1), 0) == "Make coffee"
def start_one(index):
gpu_index, region = regions[index]
scheduler = Ufo.FixedScheduler()
scheduler.set_resources(resources[index])
graph = Ufo.TaskGraph()
gpu = scheduler.get_resources().get_gpu_nodes()[gpu_index]
region_index = run_number * len(resources) + index
geometry = CTGeometry(args)
if (len(args.center_position_z) == 1 and np.modf(args.center_position_z[0])[0] == 0 and
geometry.is_simple_parallel_tomo):
LOG.info('Simple tomography with integer z center, changing to center_position_z + 0.5 '
'to avoid interpolation')
geometry.args.center_position_z = (geometry.args.center_position_z[0] + 0.5,)
if not args.disable_projection_crop:
if not args.dry_run and (args.y or args.height):
LOG.debug('--y or --height specified, not optimizing projection region')
else:
geometry.optimize_args(region=region)
opt_args = geometry.args
if args.dry_run:
source = get_task('dummy-data', number=args.number, width=args.width, height=args.height)
else:
source = None
setup_graph(opt_args, graph, x_region, y_region, region, source=source, gpu=gpu,
index=region_index, make_reader=True)
LOG.debug('Pass: %d, device: %d, region: %s', run_number + 1, gpu_index, region)
scheduler.run(graph)
return scheduler.props.time
def tweet_progress():
tasks = request.get_json()
finished = 0
for task_id in tasks:
res = get_task(task_id)
# print(res.status)
if res.ready():
finished += 1
return jsonify(finished)
def handler(chat_id, text):
if text.lstrip().startswith("/"):
if text == "/new_task":
task, answer = tasks.get_task()
_stored_chats[chat_id] = answer
return task
elif chat_id in _stored_chats:
return check_answer(chat_id, text)
return config.TEXT_NO_HANDLER
def __reset(self) -> None:
if self.__context:
self.__context.task.close()
task = get_task(self.__task_name, True)
self.__genotype = Genotype(
0,
FunctionSet(task.settings.action_number,
task.settings.perception_number))
self.__genotype.create_from_nodes(self.__chromosome)
self.__context = Phenotype.get_context(self.__genotype, task)
def tweet_result():
count = Counter({})
tasks = request.get_json()
for task_id in tasks:
res = get_task(task_id)
count += Counter(res.get())
labels = list(dict(count).keys())
total = dict(count)["total"]
data = [d / total for d in dict(count).values()]
return jsonify({"label": labels, "data": data})
async def on_message(message):
if message.content.startswith(BOT_SIGN):
command = message.content[len(BOT_SIGN):].strip()
reply = 'Unknown command: \"' + command + '\"'
if command == '':
reply = get_task()
await client.send_message(message.channel,
embed=discord.Embed(description=reply))
def airfoil_result(task_id):
task = get_task(task_id)
if task.ready():
data = task.get()
persisted_result = f"{RESULT_FOLDER}/a{data['angle']}n{data['n_nodes']}l{data['n_levels']}s{data['speed']}t{data['time']}.json"
with open(persisted_result, 'w') as outfile:
json.dump(data, outfile)
return jsonify({"status": "RESULT", "data": data})
else:
return jsonify({"status": task.status})
def __best_changed_function(self, algorithm: IAlgorithm) -> None:
if not self.best or not isinstance(self.best, IGenotype):
raise Exception('Unexpected Error')
genotype: IGenotype = cast(IGenotype, self.best)
self.__cloned_task = get_task(self.__task_name)
Phenotype.while_end(genotype, Phenotype.get_context(genotype, self.__cloned_task))
for func in self.__best_changed:
if callable(func):
func(algorithm, self.__cloned_task, self.best)
def test_get_task():
task_id = tasks.save_task({
"description": "this is a test task",
"status": "1"
})
assert type(task_id) is str
task = tasks.get_task(task_id)
print(task)
print(type(task))
assert task['description'] == "this is a test task"
def main(port):
collateral = os.getenv("COLLATERAL").split(",")
df = os.getenv("DF").split(",")
name = os.getenv("NAME").split(",")
task = os.getenv("TASK")
num_layers = int(os.getenv("NUM_LAYERS"))
hostname = socket.gethostname()
ip_address = socket.gethostbyname(hostname)
model_names = name if name and len(name) == len(collateral) else ""
Task = get_task(task, num_layers, model_names, collateral, df)
app = appConfiguration.configureApp(Task)
appConfiguration.printPageLink(hostname, port)
app.server.run(debug=True, threaded=True, host=ip_address, port=int(port))
def evaluate(args: Tuple[str, List[int], float]) -> Tuple[float, float, float]:
task_name, chromosomes, sleep = args
task = get_task(task_name)
dataset = TestDataset(task.ga_settings.test_number, TestData(task_name))
functions = FunctionSet(task.settings.action_number,
task.settings.perception_number)
genotype = Genotype(0, functions)
genotype.create_from_nodes(chromosomes)
step, action_step, fitness = Phenotype.run_episodes(genotype, dataset)
time.sleep(sleep)
return fitness, step, action_step
def __init__(self, task_name: str, *best_changed: Callable[[IAlgorithm, ITask, IChromosome], None]) -> None:
self.__task_name = task_name
self.__best_changed = best_changed
task = get_task(task_name)
settings = task.ga_settings
super().__init__(
1 if isinstance(task, AbstractAtariTask) else 3, # type: ignore
self.__best_changed_function,
self.__get_islands(task_name, task),
Termination(settings.terminate_offspring_number),
Migration(settings.migration_rate, settings.migration_interval)
)
self.__cloned_task = None
def run(config, split, checkpoint_name, output_path):
train_dir = config.train.dir
task = get_task(config)
checkpoint = utils.checkpoint.get_checkpoint(config, checkpoint_name)
last_epoch, step = utils.checkpoint.load_checkpoint(
task.get_model(), None, checkpoint)
print('from checkpoint: {} last epoch:{}'.format(checkpoint, last_epoch))
preprocess_opt = task.get_preprocess_opt()
dataloader = get_dataloader(config, split,
get_transform(config, split, **preprocess_opt))
df = inference(config, task, dataloader)
df.to_csv(output_path, index=False)
def start_one(index):
gpu_index, region = regions[index]
scheduler = Ufo.FixedScheduler()
scheduler.set_resources(resources[index])
graph = Ufo.TaskGraph()
gpu = scheduler.get_resources().get_gpu_nodes()[gpu_index]
region_index = run_number * len(resources) + index
geometry = CTGeometry(args)
if (len(args.center_position_z) == 1
and np.modf(args.center_position_z[0])[0] == 0
and geometry.is_simple_parallel_tomo):
LOG.info(
'Simple tomography with integer z center, changing to center_position_z + 0.5 '
'to avoid interpolation')
geometry.args.center_position_z = (
geometry.args.center_position_z[0] + 0.5, )
if not args.disable_projection_crop:
if not args.dry_run and (args.y or args.height):
LOG.debug(
'--y or --height specified, not optimizing projection region'
)
else:
geometry.optimize_args(region=region)
opt_args = geometry.args
if args.dry_run:
source = get_task('dummy-data',
number=args.number,
width=args.width,
height=args.height)
else:
source = None
setup_graph(opt_args,
graph,
x_region,
y_region,
region,
source=source,
gpu=gpu,
index=region_index,
make_reader=True)
LOG.debug('Pass: %d, device: %d, region: %s', run_number + 1,
gpu_index, region)
scheduler.run(graph)
return scheduler.props.time
def _setup_experiment(self):
"""Setup graphs and smiles if needed."""
smiles = ['CO', 'CCC', 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C']
n = len(smiles)
smiles_to_mol = functools.partial(
featurization.smiles_to_mol, infer_hydrogens=True)
tensorizer = featurization.MolTensorizer(preprocess_fn=smiles_to_mol)
train_index, test_index = np.arange(n - 1), np.arange(n - 1, n)
mol_list = [smiles_to_mol(smi) for smi in smiles]
x = graph_utils.smiles_to_graphs_tuple(smiles, tensorizer)
task = tasks.get_task(tasks.Task.crippen)
y = task.get_true_predictions(mol_list)
atts = task.get_true_attributions(mol_list)
exp = experiments.ExperimentData.from_data_and_splits(
x, y, atts, train_index, test_index)
model = experiments.GNN(5, 3, 10, 1, models.BlockType.gcn, 'relu',
templates.TargetType.globals, 2)
model(x)
method = techniques.CAM()
return exp, model, task, method
def generate_multireport(tasks, output_dir, task_kwargs=None, **kwargs):
"""Make a pdf report experiments either by loading them or recomputing them
on multiple tasks.
Args:
tasks (list of Task or str): list of helper objects containing meta information
of the task. If list of str, then each element should be the name of
a task which will be given to `get_task`.
output_dir (str): directory containing the different models.
task_kwargs (list of dictionnaries, optional): list of task specific arguments
that update the kwargs for a specific task.
kwargs:
Additional arguments to `generate_report` and `train`.
Returns:
models (dictionary): dictionary containing the trained model of the last
run for each task.
others (dictionary): dictionary containing additional information for the
last run of each task.
"""
models = {}
others = {}
pdf = None
print()
for i, task in enumerate(tasks):
if isinstance(task, str):
task = get_task(task)
print("----- TASK : {} -----".format(task.name))
print()
task_kwarg = task.task_kwargs
task_kwarg.update(kwargs)
if task_kwargs is not None:
task_kwarg.update(task_kwargs[i])
models[task.name], pdf, others[task.name] = generate_report(
task, output_dir, _is_multiple_tasks=True, _pdf=pdf, **task_kwarg)
pdf.close()
return models, others
def _run(self):
while not empty():
url, kwargs, callback, retries = get_task()
# Default request method to GET
kwargs.setdefault("method", "GET")
# Include our OAuth hook
kwargs.update(self.hooks)
try:
# Construct and send request
request = requests.Request(url, **kwargs)
request.send()
response = request.response
except requests.RequestException as e:
sys.stderr.write("Error requesting %s: %s, " %
(request.full_url, e.message))
if retries < self.max_retries:
# Retry...
sys.stderr.write("retrying...\n")
add_task(url, kwargs, callback, retries + 1)
else:
# Give up
sys.stderr.write("giving up...\n")
else:
# Invoke callback
if callable(callback):
callback(response, self)
# Stay within rate limits
throttle(response)
sys.stderr.write("%s exiting...\n" % str(self))
def _run(self):
while not empty():
url, kwargs, callback, retries = get_task()
# Default request method to GET
kwargs.setdefault("method", "GET")
# Include our OAuth hook
kwargs.update(self.hooks)
try:
# Construct and send request
request = requests.Request(url, **kwargs)
request.send()
response = request.response
except requests.RequestException as e:
sys.stderr.write("Error requesting %s: %s, " % (request.full_url, e.message))
if retries < self.max_retries:
# Retry...
sys.stderr.write("retrying...\n")
add_task(url, kwargs, callback, retries + 1)
else:
# Give up
sys.stderr.write("giving up...\n")
else:
# Invoke callback
if callable(callback):
callback(response, self)
# Stay within rate limits
throttle(response)
sys.stderr.write("%s exiting...\n" % str(self))
def construct_main_loop(name, task_name, batch_size, max_epochs,
patience_epochs, learning_rate,
hyperparameters, **kwargs):
task = tasks.get_task(**hyperparameters)
hyperparameters["n_channels"] = task.n_channels
extensions = []
print "constructing graphs..."
graphs, outputs, updates = construct_graphs(task=task, **hyperparameters)
print "setting up main loop..."
from blocks.model import Model
model = Model(outputs["train"]["cost"])
from blocks.algorithms import GradientDescent, CompositeRule, StepClipping, Adam
algorithm = GradientDescent(
cost=outputs["train"]["cost"],
parameters=graphs["train"].parameters,
step_rule=CompositeRule([Adam(learning_rate=learning_rate),
StepClipping(1e3)]),
on_unused_sources="warn")
algorithm.add_updates(updates["train"])
extensions.extend(construct_monitors(
algorithm=algorithm, task=task, model=model, graphs=graphs,
outputs=outputs, updates=updates, **hyperparameters))
from blocks.extensions import FinishAfter, Printing, ProgressBar, Timing
from blocks.extensions.stopping import FinishIfNoImprovementAfter
from blocks.extensions.training import TrackTheBest
from blocks.extensions.saveload import Checkpoint
from dump import DumpBest, LightCheckpoint, PrintingTo
extensions.extend([
TrackTheBest("valid_error_rate", "best_valid_error_rate"),
FinishIfNoImprovementAfter("best_valid_error_rate", epochs=patience_epochs),
FinishAfter(after_n_epochs=max_epochs),
DumpBest("best_valid_error_rate", name+"_best.zip"),
Checkpoint(hyperparameters["checkpoint_save_path"],
on_interrupt=False, every_n_epochs=5,
before_training=True, use_cpickle=True),
ProgressBar(), Timing(), Printing(), PrintingTo(name+"_log")])
from blocks.main_loop import MainLoop
main_loop = MainLoop(data_stream=task.get_stream("train"),
algorithm=algorithm,
extensions=extensions,
model=model)
# note blocks will crash and burn because it cannot deal with an
# already-initialized Algorithm, so this should be enabled only for
# debugging
if False:
with open("graph", "w") as graphfile:
algorithm.initialize()
theano.printing.debugprint(algorithm._function, file=graphfile)
from tabulate import tabulate
print "parameter sizes:"
print tabulate((key, "x".join(map(str, value.get_value().shape)), value.get_value().size)
for key, value in main_loop.model.get_parameter_dict().items())
return main_loop
def construct_main_loop(name, task_name, patch_shape, batch_size,
n_spatial_dims, n_patches, max_epochs, patience_epochs,
learning_rate, gradient_limiter, hyperparameters,
**kwargs):
task = tasks.get_task(**hyperparameters)
hyperparameters["n_channels"] = task.n_channels
extensions = []
# let theta noise decay as training progresses
for key in "location_std scale_std".split():
hyperparameters[key] = theano.shared(hyperparameters[key], name=key)
extensions.append(
util.ExponentialDecay(hyperparameters[key],
hyperparameters["%s_decay" % key],
after_batch=True))
print "constructing graphs..."
graphs, outputs, updates = construct_graphs(task=task, **hyperparameters)
print "setting up main loop..."
from blocks.model import Model
model = Model(outputs["train"]["cost"])
from blocks.algorithms import GradientDescent, CompositeRule, StepClipping, Adam, RMSProp
from extensions import Compressor
if gradient_limiter == "clip":
limiter = StepClipping(1.)
elif gradient_limiter == "compress":
limiter = Compressor()
else:
raise ValueError()
algorithm = GradientDescent(
cost=outputs["train"]["cost"],
parameters=graphs["train"].parameters,
step_rule=CompositeRule([limiter,
Adam(learning_rate=learning_rate)]))
algorithm.add_updates(updates["train"])
extensions.extend(
construct_monitors(algorithm=algorithm,
task=task,
model=model,
graphs=graphs,
outputs=outputs,
updates=updates,
**hyperparameters))
from blocks.extensions import FinishAfter, Printing, ProgressBar, Timing
from blocks.extensions.stopping import FinishIfNoImprovementAfter
from blocks.extensions.training import TrackTheBest
from blocks.extensions.saveload import Checkpoint
from dump import DumpBest, LightCheckpoint, PrintingTo, DumpGraph, DumpLog
extensions.extend([
TrackTheBest("valid_error_rate", "best_valid_error_rate"),
FinishIfNoImprovementAfter("best_valid_error_rate",
epochs=patience_epochs),
FinishAfter(after_n_epochs=max_epochs),
DumpBest("best_valid_error_rate", name + "_best.zip"),
Checkpoint(hyperparameters["checkpoint_save_path"],
on_interrupt=False,
every_n_epochs=10,
use_cpickle=True),
DumpLog("log.pkl", after_epoch=True),
ProgressBar(),
Timing(),
Printing(),
PrintingTo(name + "_log"),
DumpGraph(name + "_grad_graph")
])
from blocks.main_loop import MainLoop
main_loop = MainLoop(data_stream=task.get_stream("train"),
algorithm=algorithm,
extensions=extensions,
model=model)
from tabulate import tabulate
print "parameter sizes:"
print tabulate(
(key, "x".join(map(str,
value.get_value().shape)), value.get_value().size)
for key, value in main_loop.model.get_parameter_dict().items())
return main_loop
def hello():
return render_template('dash.html', tasks=tasks.get_task())
def prepare_tasks():
result = tasks.get_task()
print result
return simplejson.dumps({"result": result})
def main(_):
# set up logger
tf.logging.set_verbosity(tf.logging.INFO)
tf.logging.info("Welcome Using Zero :)")
params = global_params
# try loading parameters
# priority: command line > saver > default
# 1. load latest path to load parameters
if os.path.exists(flags.FLAGS.config):
params.override_from_dict(eval(open(flags.FLAGS.config).read()))
params = load_parameters(params, params.output_dir)
# 2. refine with command line parameters
if os.path.exists(flags.FLAGS.config):
params.override_from_dict(eval(open(flags.FLAGS.config).read()))
params.parse(flags.FLAGS.parameters)
# set up random seed
random.seed(params.random_seed)
np.random.seed(params.random_seed)
tf.set_random_seed(params.random_seed)
# loading vocabulary
tf.logging.info("Begin Loading Vocabulary")
start_time = time.time()
full_task = get_task(params, True)
if not os.path.exists(params.word_vocab_file):
params.word_vocab = Vocab(lower=params.lower)
params.word_vocab.make_vocab(
full_task,
use_char=False,
embedding_path=params.pretrain_word_embedding_file)
else:
params.word_vocab = Vocab(lower=params.lower,
vocab_file=params.word_vocab_file)
if params.use_char:
if not os.path.exists(params.char_vocab_file):
params.char_vocab = Vocab(lower=False)
params.char_vocab.make_vocab(full_task,
use_char=True,
embedding_path=None)
else:
params.char_vocab = Vocab(lower=False,
vocab_file=params.char_vocab_file)
tf.logging.info("End Loading Vocabulary, Word Vocab Size {}, "
"Char Vocab Size {}, within {} seconds".format(
params.word_vocab.size(),
params.char_vocab.size() if params.use_char else 0,
time.time() - start_time))
if flags.FLAGS.mode == "vocab":
save_parameters(params, params.output_dir)
return
# save parameters
if flags.FLAGS.mode == "train":
save_parameters(params, params.output_dir)
# loading bert config
if params.enable_bert:
bert_config = bert.load_config(params.bert_dir)
params.bert = tc.training.HParams(**bert_config)
# loading vocabulary
tf.logging.info("Begin Loading Vocabulary")
start_time = time.time()
params.bert.vocab = bert.load_vocab(params.bert_dir)
tf.logging.info(
"End Loading Vocabulary, Vocab Size {}, within {} seconds".format(
params.bert.vocab.size,
time.time() - start_time))
# loading task label information
params.label_size = full_task.get_label_size()
# print parameters
print_parameters(params)
# print the used datasets
tf.logging.info("Task {} is performed with data {}".format(
params.task, full_task.data_path))
mode = flags.FLAGS.mode
if mode == "train":
# load the recorder
params = setup_recorder(params)
graph.train(params)
elif mode == "test":
graph.evaluate(params)
else:
tf.logging.error("Invalid mode: {}".format(mode))
def test_create():
con = psycopg2.connect(**DATABASE)
tasks.add_task(con, datetime.date(2020, 4, 1), "Wake up")
assert tasks.get_task(con, datetime.date(2020, 4, 1), 1) == "Wake up"
def test_delete():
con = psycopg2.connect(**DATABASE)
tasks.add_task(con, datetime.date(2020, 4, 1), "Wake up")
tasks.delete_task(con, datetime.date(2020, 4, 1), 1)
with pytest.raises(TypeError):
tasks.get_task(con, datetime.date(2020, 4, 1), 1)
def test_update():
con = psycopg2.connect(**DATABASE)
tasks.add_task(con, datetime.date(2020, 4, 1), "Wake up")
tasks.edit_task(con, datetime.date(2020, 4, 1), 1, "Make coffee")
assert tasks.get_task(con, datetime.date(2020, 4, 1), 1) == "Make coffee"
def construct_main_loop(name, task_name, patch_shape, batch_size,
n_spatial_dims, n_patches, max_epochs,
patience_epochs, learning_rate, gradient_limiter,
hyperparameters, **kwargs):
task = tasks.get_task(**hyperparameters)
hyperparameters["n_channels"] = task.n_channels
extensions = []
# let theta noise decay as training progresses
for key in "location_std scale_std".split():
hyperparameters[key] = theano.shared(hyperparameters[key], name=key)
extensions.append(util.ExponentialDecay(
hyperparameters[key],
hyperparameters["%s_decay" % key],
after_batch=True))
print "constructing graphs..."
graphs, outputs, updates = construct_graphs(task=task, **hyperparameters)
print "setting up main loop..."
from blocks.model import Model
model = Model(outputs["train"]["cost"])
from blocks.algorithms import GradientDescent, CompositeRule, StepClipping, Adam, RMSProp
from extensions import Compressor
if gradient_limiter == "clip":
limiter = StepClipping(1.)
elif gradient_limiter == "compress":
limiter = Compressor()
else:
raise ValueError()
algorithm = GradientDescent(
cost=outputs["train"]["cost"],
parameters=graphs["train"].parameters,
step_rule=CompositeRule([limiter, Adam(learning_rate=learning_rate)]))
algorithm.add_updates(updates["train"])
extensions.extend(construct_monitors(
algorithm=algorithm, task=task, model=model, graphs=graphs,
outputs=outputs, updates=updates, **hyperparameters))
from blocks.extensions import FinishAfter, Printing, ProgressBar, Timing
from blocks.extensions.stopping import FinishIfNoImprovementAfter
from blocks.extensions.training import TrackTheBest
from blocks.extensions.saveload import Checkpoint
from dump import DumpBest, LightCheckpoint, PrintingTo, DumpGraph, DumpLog
extensions.extend([
TrackTheBest("valid_error_rate", "best_valid_error_rate"),
FinishIfNoImprovementAfter("best_valid_error_rate", epochs=patience_epochs),
FinishAfter(after_n_epochs=max_epochs),
DumpBest("best_valid_error_rate", name+"_best.zip"),
Checkpoint(hyperparameters["checkpoint_save_path"],
on_interrupt=False, every_n_epochs=10,
use_cpickle=True),
DumpLog("log.pkl", after_epoch=True),
ProgressBar(),
Timing(),
Printing(), PrintingTo(name+"_log"),
DumpGraph(name+"_grad_graph")])
from blocks.main_loop import MainLoop
main_loop = MainLoop(data_stream=task.get_stream("train"),
algorithm=algorithm,
extensions=extensions,
model=model)
from tabulate import tabulate
print "parameter sizes:"
print tabulate((key, "x".join(map(str, value.get_value().shape)), value.get_value().size)
for key, value in main_loop.model.get_parameter_dict().items())
return main_loop
def runnings_backups():
task = get_task()
is_runnig = (task != None)
finish = ( is_runnig and task.get() != None)
return is_runnig and not finish
def args2tasks(args):
"""Given the parsed arguments, return teh correct list of tasks."""
kwargs = {}
if args.mode == "small":
kwargs["is_small"] = True
elif args.mode == "mini":
kwargs["is_mini"] = True
if args.tasks == "important":
tasks = [
get_task("long lookup", **kwargs),
get_task("long lookup reverse", **kwargs),
get_task("noisy long lookup single", **kwargs),
get_task("long lookup intermediate noise", **kwargs),
get_task("noisy long lookup multi", **kwargs),
get_task("scan", **kwargs),
get_task("symbol rewriting", is_small=True)
]
elif args.tasks == "all":
tasks = [
get_task("lookup", **kwargs),
get_task("long lookup", **kwargs),
get_task("long lookup jump", **kwargs),
get_task("long lookup oneshot", **kwargs),
get_task("long lookup reverse", **kwargs),
get_task("noisy long lookup single", **kwargs),
get_task("long lookup intermediate noise", **kwargs),
get_task("noisy long lookup multi", **kwargs),
get_task("scan", **kwargs),
get_task("symbol rewriting", **kwargs)
]
else:
tasks = [
get_task(task.replace("_", " "), **kwargs) for task in args.tasks
]
# will be removed after because None
args.tasks = None
args.mode = None
return tasks
def test_create():
tasks.add_task(datetime.date(2020, 4, 1), "Wake up")
assert tasks.get_task(datetime.date(2020, 4, 1), 0) == "Wake up"
def test_delete():
tasks.add_task(datetime.date(2020, 4, 1), "Wake up")
tasks.delete_task(datetime.date(2020, 4, 1), 0)
with pytest.raises(KeyError):
tasks.get_task(datetime.date(2020, 4, 1), 0)