def __wait(self):
"""Wait on waitable started tasks in this manager."""
for obj in self.__tasks:
if obj._state == RUNNING and hasattr(obj, "wait") and obj.wait:
assert obj._manager == self
with Progress("Waiting on %s" % obj.name):
self.__callMeMethod(obj.wait)
class SearchTerm:
def __init__(self, filename):
words = filter(bool, open(filename, 'r').read().split('\n'))
# Record and store progress
progress_filename = filename + '.progress'
self.progress = Progress(current_file = progress_filename)
# Load progress
if self.progress.current:
self.word_list = words[self.progress.current[0]:]
else:
self.word_list = words
self.counter = 0
def current(self):
"""
the index of word in word list
"""
return self.progress.current
def get_counter(self):
"""
times next() has been called, ie. progress of current session.
"""
return self.counter
def next(self):
self.progress.next([0], [len(self.word_list)])
self.progress.save()
self.counter += 1
def get_word_list(self):
return self.word_list
def expand_word_list(self, expand_type):
if expand_type == "suggest":
self.google_suggest()
elif expand_type == "search":
None
else:
None
def collect(self):
None
def google_suggest(self):
None
def upload(path):
file_size = os.stat(path).st_size
if file_size <= 5 * 1024 * 1024:
url = get_signed_url(path, "PUT")
progress = Progress()
stream = FileWithCallback(path, 'rb', progress.update, path)
response = requestor.session.put(url, data=stream)
return response
else:
return multipart_upload(path)
def __init__(self, filename):
words = filter(bool, open(filename, 'r').read().split('\n'))
# Record and store progress
progress_filename = filename + '.progress'
self.progress = Progress(current_file = progress_filename)
# Load progress
if self.progress.current:
self.word_list = words[self.progress.current[0]:]
else:
self.word_list = words
self.counter = 0
def test_Progress(): # multiple values progress = Progress(current_file='../../data/trend/no_file') assert_equal(progress.next([8,0,0,0,0], [10,9,9,9,9]), [9,0,0,0,0]) assert_equal(progress.next([8,0,0,0,0], [10,9,9,9,9]), [8,1,0,0,0]) assert_equal(progress.next([8,0,0,0,0], [10,9,9,9,9]), [9,1,0,0,0]) # single value progress = Progress(current_file='../../data/trend/no_file', start=[0]) assert_equal(progress.next([0], [3]), [1]) assert_equal(progress.next([0], [3]), [2]) assert_equal(progress.next([0], [3]), None) # start from middle progress = Progress(current_file='../../data/trend/no_file', start=[3]) assert_equal(progress.next([0], [6]), [4]) assert_equal(progress.next([0], [6]), [5]) assert_equal(progress.next([0], [6]), None)
def __stop(self):
"""Stop all running tasks in this manager in reverse of the
order they were started in."""
for obj in reversed(self.__tasks):
if obj._state == STOPPED:
continue
assert obj._manager == self
if hasattr(obj, "stop") and obj.stop:
with Progress("Stopping %s" % obj.name):
self.__callMeMethod(obj.stop)
obj._state = STOPPED
obj._manager = None
def __start(self):
"""Start all tasks in this manager."""
for obj in self.__tasks:
if obj._state == RUNNING:
if obj._manager != self:
raise ValueError("Task %s is running in another manager" %
obj.name)
continue
if hasattr(obj, "start") and obj.start:
with Progress("Starting %s" % obj.name):
self.__callMeMethod(obj.start)
obj._state = RUNNING
obj._manager = self
def sampleAndGetStreetImageLinks(endPoints, sampleNum, picNum, ptrNum, intersectionPointInfo):
"""
Randomly select end points from the endPoint collection.
For each selected end point, call Google map street view image api
to get the street view images.
:return:
"""
print "sampling street images..."
# get 2x sampled points for skipping some images that are missing its date
sampledPoints = random.sample(endPoints, sampleNum) if sampleNum < len(endPoints) * 2 else endPoints
sampleData = [] # store (picture number, file name, lat and lng, link to image)
progress = Progress(10)
headings = CONFIG["gmap"]["headings"]
sampleNumDelta = len(headings)
for point in sampledPoints:
progress.printProgress()
result = getSurroundingStreetViewLinks(point, picNum, ptrNum, intersectionPointInfo)
sampleData += result
picNum += sampleNumDelta
ptrNum += 1
print ""
return sampleData
def sampleAndDownloadStreetImage(endPoints, sampleNum, picNum, ptrNum,
targetDirectory, intersectionPointInfo):
"""
Randomly select end points from the endPoint collection.
For each selected end point, call Google map street view image api
to get the street view images.
:return:
"""
print "downloading street images..."
sampledPoints = random.sample(
endPoints, sampleNum) if sampleNum < len(endPoints) else endPoints
sampleData = [] # store (picture number, file name, lat and lng)
progress = Progress(10)
headings = CONFIG["gmap"]["headings"]
sampleNumDelta = len(headings)
for point in sampledPoints:
progress.printProgress()
result = downloadSurroundingStreetView(point, targetDirectory, picNum,
ptrNum, intersectionPointInfo)
sampleData += result
picNum += sampleNumDelta
ptrNum += 1
print ""
return sampleData
def __reset(self):
"""Reset all tasks in this manager in their stop order. Tasks
are reset regardless of their current state and are always put
in the STOPPED state. Exceptions will be printed and
ignored."""
for obj in reversed(self.__tasks):
assert obj._manager == None or obj._manager == self
if hasattr(obj, "reset") and obj.reset:
with Progress("Resetting %s" % obj.name):
try:
self.__callMeMethod(obj.reset)
except:
sys.excepthook(*sys.exc_info())
obj._state = STOPPED
obj._manager = None
def wait_error():
progress = Progress(20)
for i in range(21):
if i: progress.increment()
time.sleep(ERROR_TIME / 21.0)
progress.done()
def train(train_story, train_questions, train_qstory, memory, model, loss,
general_config):
train_config = general_config.train_config
dictionary = general_config.dictionary
nepochs = general_config.nepochs
nhops = general_config.nhops
batch_size = general_config.batch_size
enable_time = general_config.enable_time
randomize_time = general_config.randomize_time
lrate_decay_step = general_config.lrate_decay_step
train_range = general_config.train_range # indices of training questions
val_range = general_config.val_range # indices of validation questions
train_len = len(train_range)
val_len = len(val_range)
params = {
"lrate": train_config["init_lrate"],
"max_grad_norm": train_config["max_grad_norm"]
}
for ep in range(nepochs):
# Decrease learning rate after every decay step
if (ep + 1) % lrate_decay_step == 0:
params["lrate"] *= 0.5
total_err = 0.
total_cost = 0.
total_num = 0
# print train_len
# print(train_len, batch_size, int(math.floor(train_len / batch_size)))
for _ in Progress(range(int(math.floor(train_len / batch_size)))):
# Question batch
batch = train_range[np.random.randint(train_len, size=batch_size)]
input_data = np.zeros((train_story.shape[0], batch_size),
np.float32) # words of training questions
target_data = train_questions[2,
batch] # indices of training answers
memory[0].data[:] = dictionary["nil"]
# Compose batch of training data
for b in range(batch_size):
# NOTE: +1 since train_questions[1, :] is the index of the sentence right before the training question.
# d is a batch of [word indices in sentence, sentence indices from batch] for this story
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]]
# Pick a fixed number of latest sentences (before the question) from the story
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:]
# Training data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d
if enable_time:
# Inject noise into time index (i.e. word index)
if randomize_time > 0:
# Random number of blank (must be < total sentences until the training question?)
nblank = np.random.randint(
int(math.ceil(d.shape[1] * randomize_time)))
rt = np.random.permutation(d.shape[1] + nblank)
rt[rt >= train_config["sz"]] = train_config[
"sz"] - 1 # put the cap
# Add random time (must be > dictionary's length) into the time word (decreasing order)
memory[0].data[-1, :d.shape[1], b] = np.sort(
rt[:d.shape[1]])[::-1] + len(dictionary)
else:
memory[0].data[-1, :d.shape[1], b] = \
np.arange(d.shape[1])[::-1] + len(dictionary)
input_data[:, b] = train_qstory[:, batch[b]]
for i in range(1, nhops):
memory[i].data = memory[0].data
out = model.fprop(input_data)
total_cost += loss.fprop(out, target_data)
total_err += loss.get_error(out, target_data)
total_num += batch_size
grad = loss.bprop(out, target_data)
model.bprop(input_data, grad)
model.update(params)
for i in range(nhops):
memory[i].emb_query.weight.D[:, 0] = 0
# Validation
total_val_err = 0.
total_val_cost = 0.
total_val_num = 0
for k in range(int(math.floor(val_len / batch_size))):
batch = val_range[np.arange(k * batch_size, (k + 1) * batch_size)]
input_data = np.zeros((train_story.shape[0], batch_size),
np.float32)
target_data = train_questions[2, batch]
memory[0].data[:] = dictionary["nil"]
for b in range(batch_size):
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]]
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:]
# Data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d
if enable_time:
memory[0].data[-1, :d.shape[1], b] = np.arange(
d.shape[1])[::-1] + len(dictionary)
input_data[:, b] = train_qstory[:, batch[b]]
for i in range(1, nhops):
memory[i].data = memory[0].data
out = model.fprop(input_data)
total_val_cost += loss.fprop(out, target_data)
total_val_err += loss.get_error(out, target_data)
total_val_num += batch_size
train_error = total_err / total_num
val_error = total_val_err / total_val_num
print("%d | train error: %g | val error: %g" %
(ep + 1, train_error, val_error))
def threshold_table(start,
stop,
reading_channels,
channels,
bands,
label='kmeans-labels',
filename=DEFAULT_FILENAME,
prefix='.'):
"""
Makes a html table of 'percent increase' from the largest cluster by band and channel.
"""
data = TimeSeriesDict.read(filename,
reading_channels + [label],
start=to_gps(start),
end=to_gps(stop))
labels = data[label]
clusters = list(range(max(labels.value) + 1))
cluster_counts = list(
len(labels.value[labels.value == c]) for c in clusters)
largest_cluster = cluster_counts.index(max(cluster_counts))
clusters.remove(largest_cluster)
logger.info(
f'Largest cluster found to be Nº{largest_cluster} ({100 * max(cluster_counts) // len(labels.value)}%). Doing {clusters}.'
)
cluster_counts.remove(max(cluster_counts))
def amplitude(channel, cluster):
"""return median amplitude for channel in cluster."""
try:
chan = data[channel]
except KeyError:
return 0.0
return median([
chan.value[i] for i, c in enumerate(labels.value) if c == cluster
])
def threshold(cluster, channel, band) -> str:
f_channel = f'{channel}_BLRMS_{band}.mean'
base = amplitude(f_channel, largest_cluster)
if base != 0.0:
return str(int(
100 * (amplitude(f_channel, cluster) - base) / base)) + '%'
else:
return str(amplitude(f_channel, cluster))
range_chan = 'L1:DMT-SNSH_EFFECTIVE_RANGE_MPC.mean'
if range_chan in reading_channels:
base_range = amplitude(range_chan, largest_cluster)
if base_range != 0.0:
snsh = lambda c: 'SNSH: ' + str(
int(100 * (amplitude(range_chan, c) - base_range) / base_range)
) + '%'
else:
snsh = lambda c: 'SNSH: 0.0'
else:
snsh = lambda c: ''
with Progress('taking thresholds', len(clusters)) as progress:
for i, cluster in enumerate(clusters):
buffer = [[''] + bands]
for channel in channels:
buffer.append([channel] + [
progress(threshold, i, cluster, channel, band)
for band in bands
])
html_table(
f'cluster {cluster} ({colors[cluster]}) {snsh(cluster)}',
csv_writer(buffer, get_path(f'{cluster}', 'csv',
prefix=prefix)),
get_path(f'{cluster}', 'html', prefix=prefix))
html_table(
'Index',
csv_writer(
[['clusters:']] +
[[f'<a href="{cluster}.html">Nº{cluster} ({colors[cluster]})</a>']
for cluster in clusters], get_path('idx', 'csv', prefix=prefix)),
get_path('index', 'html', prefix=prefix))
def compute_kmeans(channels,
start,
stop,
history=timedelta(hours=2),
filename=DEFAULT_FILENAME,
downloader=TimeSeriesDict.get,
**kwargs):
"""
Computes k-means clusters and saves the data and labels to filename.
**kwargs are forwarded to the KMeans constructor.
>>> from gwpy.time import tconvert, from_gps
>>> from datetime import timedelta
>>> from cluster import compute_kmeans
>>>
>>> channels = [f'L1:ISI-GND_STS_ETMX_Z_BLRMS_1_3.mean,m-trend', 'L1:ISI-GND_STS_ETMY_Z_BLRMS_1_3.mean,m-trend']
>>>
>>> stop = from_gps(60 * (int(tconvert('now')) // 60)) # gets nearest minute to now
>>> start = stop - timedelta(days=1) # cluster the past day
>>> compute_kmeans(channels, start, stop, filename='my_kmeans.hdf5', n_clusters=5, random_state=0)
"""
# set up duration (minute-trend data has dt=1min, so reject intervals not on the minute).
duration = (stop - start).total_seconds() / 60
assert (stop - start).total_seconds() / 60 == (stop -
start).total_seconds() // 60
duration = int(duration)
logger.info(
f'Clustering data from {start} to {stop} ({duration} minutes).')
# download data using TimeSeries.get(), including history of point at t0.
logger.debug(
f'Initiating download from {start} to {stop} with history={history}...'
)
dl = downloader(channels, start=to_gps(start - history), end=to_gps(stop))
logger.info(f'Downloaded from {start} to {stop} with history={history}.')
# generate input matrix of the form [sample1;...;sampleN] with sampleK = [feature1,...,featureN]
# for sklearn.cluster algorithms. This is the slow part of the function, so a progress bar is shown.
logger.debug(f'Initiating input matrix generation...')
with Progress('building input', (duration * 60)) as progress:
input_data = stack([
concatenate([
progress(dl[channel].crop,
t,
start=to_gps(start + timedelta(seconds=t) - history),
end=to_gps(start + timedelta(seconds=t))).value
for channel in channels
]) for t in range(0, int(duration * 60), 60)
])
# verify input matrix dimensions.
assert input_data.shape == (duration,
int(
len(channels) * history.total_seconds() /
60))
logger.info('Completed input matrix generation.')
# actually do the fit.
logger.debug(f'Initiating KMeans({kwargs}) fit...')
kmeans = KMeans(**kwargs).fit(input_data)
logger.info(f'Completed KMeans({kwargs}) fit.')
# cast the output labels to a TimeSeries so that cropping is easy later on.
labels = TimeSeries(kmeans.labels_,
times=dl[channels[0]].crop(start=to_gps(start),
end=to_gps(stop)).times,
name='kmeans-labels')
# put labels in data download dictionary for easy saving.
dl[labels.name] = labels
# write data download and labels to specified filename.
cache_file = abspath(filename)
if exists(cache_file):
remove(cache_file)
dl.write(cache_file)
logger.info(f'Wrote cache to {filename}')
def cluster_plotter(channels,
start,
stop,
prefix='.',
label='kmeans-labels',
groups=None,
filename=DEFAULT_FILENAME,
dqflag='L1:DMT-ANALYSIS_READY:1',
xscale=None,
unit=None,
progressbar=True,
**kwargs):
"""
Plots data with clusters labeled by color in the working directory, or a relative path given by prefix.
Requires a .hdf5 file produced with a clustering function defined in this module to be in the working directory.
**kwargs are forwarded to TimeSeries.plot().
:param prefix: relative path to output images.
:param label: name attribute of labels TimeSeries saved in filename.
:param groups: groups of channels to plot in the same figure. See the example.
:param dqflag: data quality flag for segments bar.
:param xscale: gps x-axis scale to use.
:param unit: override y-axis unit.
:param progressbar: show progress bar.
>>> from gwpy.time import tconvert, from_gps
>>> from datetime import timedelta
>>> from cluster import cluster_plotter
>>>
>>> channels = [f'L1:ISI-GND_STS_ETMX_Z_BLRMS_1_3.mean,m-trend', 'L1:ISI-GND_STS_ETMY_Z_BLRMS_1_3.mean,m-trend']
>>> groups = [[channels, ('ETMX', 'ETMY'), 'L1:ISI-GND_STS_BLRMS_1_3 Z-axis']] # plot on the same figure.
>>>
>>> stop = from_gps(60 * (int(tconvert('now')) // 60)) # gets nearest minute to now
>>> start = stop - timedelta(days=1) # cluster the past day
>>> cluster_plotter(channels, start, stop, filename='my_kmeans.hdf5', groups=groups)
"""
# some defaults.
if not kwargs:
kwargs['color'] = 'k'
kwargs['alpha'] = 0.3
if groups is None:
groups = channels
# read the data from the save file.
data = TimeSeriesDict.read(filename,
channels + [label],
start=to_gps(start),
end=to_gps(stop))
logger.info(f'Read {start} to {stop} from {filename}')
# get segments for the duration specified. Note that this may require doing `ligo-proxy-init -p`.
logger.debug(f'Getting segments for {dqflag} from {start} to {stop}...')
dq = DataQualityFlag.query(dqflag, to_gps(start), to_gps(stop))
logger.info(f'Got segments for {dqflag} from {start} to {stop}.')
# plotting is slow, so show a nice progress bar.
logger.debug('Initiating plotting routine...')
with Progress('plotting', len(channels),
quiet=not progressbar) as progress:
for p, (group, labels, title) in enumerate(groups):
# plot the group in one figure.
plt = Plot(*(data[channel] for channel in group),
separate=True,
sharex=True,
zorder=1,
**kwargs)
# modify the axes one by one.
axes = plt.get_axes()
for i, ax in enumerate(axes):
# namely, add a colored overlay that indicates clustering labels.
ax.scatter(data[group[i]].times,
data[group[i]].value,
c=[colors[j] for j in data[label]],
edgecolor='',
s=4,
zorder=2)
ax.set_ylabel(
f'{labels[i]} {data[group[i]].unit if unit is None else unit}'
)
setp(ax.get_xticklabels(), visible=False)
# modify the figure as a whole.
plt.add_segments_bar(dq, label='')
if xscale is not None:
plt.gca().set_xscale(xscale)
plt.suptitle(title)
# save to png.
progress(plt.save, p, get_path(title, 'png', prefix=prefix))
logger.info(f'Completed plotting for {start} to {stop} from {filename}')
def train(train_story,
train_questions,
train_qstory,
memory,
model,
loss_function,
general_config,
USE_CUDA=False):
FloatTensor = torch.cuda.FloatTensor if USE_CUDA else torch.FloatTensor
LongTensor = torch.cuda.LongTensor if USE_CUDA else torch.LongTensor
ByteTensor = torch.cuda.ByteTensor if USE_CUDA else torch.ByteTensor
train_config = general_config.train_config
dictionary = general_config.dictionary
nepochs = general_config.nepochs
nhops = general_config.nhops
batch_size = general_config.batch_size
enable_time = general_config.enable_time
randomize_time = general_config.randomize_time
lrate_decay_step = general_config.lrate_decay_step
train_range = general_config.train_range # indices of training questions
val_range = general_config.val_range # indices of validation questions
train_len = len(train_range)
val_len = len(val_range)
params = {
"lrate": train_config["init_lrate"],
"max_grad_norm": train_config["max_grad_norm"]
}
optimizer = optim.SGD(model.parameters(), lr=params["lrate"])
for ep in range(nepochs):
# Decrease learning rate after every decay step
if (ep + 1) % lrate_decay_step == 0:
params["lrate"] *= 0.5
for param_group in optimizer.param_groups:
param_group['lr'] = params["lrate"]
total_err = 0.
total_cost = 0.
total_num = 0
for _ in Progress(range(int(math.floor(train_len / batch_size)))):
# Question batch
# batch = train_range[np.random.randint(train_len, size=batch_size)]
batch = train_range[torch.randint(train_len, size=(batch_size, ))]
#batch = train_range
input_data = Variable(
torch.zeros((train_story.shape[0], batch_size),
dtype=torch.float32))
input_data.requires_grad = False
target_data = Variable(train_questions[2, batch])
with torch.no_grad():
memory[0].data[:] = dictionary["nil"]
# Compose batch of training data
with torch.no_grad():
for b in range(batch_size):
# NOTE: +1 since train_questions[1, :] is the index of the sentence right before the training question.
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]].detach()
# Pick a fixed number of latest sentences (before the question) from the story
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:].detach()
# Training data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d.detach()
if enable_time:
# Inject noise into time index (i.e. word index)
if randomize_time > 0:
# Random number of blank (must be < total sentences until the training question?)
nblank = np.random.randint(
int(math.ceil(d.shape[1] * randomize_time)))
rt = np.random.permutation(d.shape[1] + nblank)
rt[rt >= train_config["sz"]] = train_config[
"sz"] - 1 # put the cap
# Add random time (must be > dictionary's length) into the time word (decreasing order)
nparray = np.sort(rt[:d.shape[1]])[::-1] + len(
dictionary, )
with torch.no_grad():
memory[0].data[-1, :d.shape[1],
b] = torch.from_numpy(
nparray).detach()
else:
memory[0].data[
-1, :d.shape[1], b] = torch.from_numpy(
np.arange(d.data.numpy().shape[1])[::-1] +
len(dictionary))
input_data[:, b] = train_qstory[:, batch[b]].detach()
for i in range(1, nhops):
with torch.no_grad():
memory[i].data = memory[0].data
#input_data.requires_grad_()
model.zero_grad()
for i in memory:
memory[i].zero_grad()
memory[i].mod_out.zero_grad()
memory[i].mod_query.zero_grad()
optimizer.zero_grad()
out = model(input_data)
loss = loss_function(out.view(out.shape[1], -1), target_data)
total_cost += loss.item()
y = out.max(0)[1] # y = out.argmax(axis=0)
total_err += torch.sum(
y != target_data) # total_err += np.sum(y != target_data)
total_num += batch_size
loss.backward()
torch.nn.utils.clip_grad_norm_(model.parameters(),
params["max_grad_norm"],
norm_type=2)
optimizer.step()
with torch.no_grad():
for i in range(nhops):
memory[i].emb_query.weight[:, 0] = 0
# Validation
total_val_err = 0.
total_val_cost = 0.
total_val_num = 0
#input_data.requires_grad_()
for k in range(int(math.floor(val_len / batch_size))):
batch = val_range[torch.arange(
k * batch_size, (k + 1) * batch_size
)] # val_range[np.arange(k * batch_size, (k + 1) * batch_size)]
input_data = torch.zeros(
(train_story.shape[0], batch_size), dtype=torch.float32
) # input_data = np.zeros((train_story.shape[0], batch_size), np.float32)
target_data = train_questions[2, batch]
memory[0].data[:] = dictionary["nil"]
for b in range(batch_size):
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]]
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:]
# Data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d
if enable_time:
tensor = torch.arange(d.shape[1])
idx = [i for i in range(tensor.size(0) - 1, -1, -1)]
idx = torch.LongTensor(idx)
inverted_tensor = tensor.index_select(
0, idx) + len(dictionary)
memory[0].data[
-1, :d.shape[1],
b] = inverted_tensor # np.arange(d.shape[1])[::-1] + len(dictionary)
input_data[:, b] = train_qstory[:, batch[b]]
for i in range(1, nhops):
memory[i].data = memory[0].data
out = model(input_data)
loss = loss_function(out.view(out.shape[1], -1), target_data)
total_val_cost += loss.item()
y = out.max(0)[1] # y = out.argmax(axis=0)
total_val_err += torch.sum(
y != target_data) # total_err += np.sum(y != target_data)
total_val_num += batch_size
train_error = total_err.float() / total_num
val_error = total_val_err.float() / total_val_num
print("%d | train error: %g | val error: %g" %
(ep + 1, train_error, val_error))
def representative_spectra(channels,
start,
stop,
rate,
label='kmeans-labels',
filename=DEFAULT_FILENAME,
prefix='.',
downloader=TimeSeriesDict.get,
cluster_numbers=None,
groups=None,
**kwargs):
"""
Make representative spectra for each cluster based on the median psd for minutes in that cluster.
Downloads only the raw minutes in the cluster to save.
"""
if groups is None:
groups = channels
# read the labels from the save file.
labels = TimeSeries.read(filename,
label,
start=to_gps(start),
end=to_gps(stop))
logger.info(f'Read labels {start} to {stop} from {filename}')
if cluster_numbers is None:
clusters = list(range(max(labels.value) + 1))
cluster_counts = list(
len(labels.value[labels.value == c]) for c in clusters)
largest_cluster = cluster_counts.index(max(cluster_counts))
clusters.remove(largest_cluster)
logger.info(
f'Largest cluster found to be Nº{largest_cluster} ({100 * max(cluster_counts) // len(labels.value)}%). Doing {clusters}.'
)
cluster_counts.remove(max(cluster_counts))
else:
clusters = cluster_numbers
cluster_counts = list(
len(labels.value[labels.value == c]) for c in clusters)
t, v, d = labels.times, labels.value, diff(labels.value)
pairs = list(
zip([t[0]] + list(t[:-1][d != 0]),
list(t[1:][d != 0]) + [t[-1]]))
values = list(v[:-1][d != 0]) + [v[-1]]
assert len(pairs) == len(values) # need to include start-| and |-end
# l|r l|r l|r l|r
# l,r l,r l,r l,r
# l r,l r,l r,l r # zip(start + l[1:], r[:-1] + stop)
print(pairs)
for pair in pairs:
print(int(pair[1].value) - int(pair[0].value))
print(values)
# use h5py to make a mutable object pointing to a file on disk.
save_file, filename = path2h5file(
get_path(f'spectra-cache {start}', 'hdf5', prefix=prefix))
logger.debug(f'Initiated hdf5 stream to {filename}')
logger.info(f'Patching {filename}...')
for i, (dl_start, end) in enumerate(pairs):
if values[i] in clusters:
if not data_exists(channels, to_gps(end).seconds, save_file):
logger.debug(
f'Downloading Nº{values[i]} from {dl_start} to {end}...')
try:
dl = downloader(channels,
start=to_gps(dl_start) - LIGOTimeGPS(60),
end=to_gps(end) + LIGOTimeGPS(seconds=1))
out = TimeSeriesDict()
for n in dl:
out[n] = dl[n].resample(**better_aa_opts(dl[n], rate))
write_to_disk(out, to_gps(dl_start).seconds, save_file)
except RuntimeError: # Cannot find all relevant data on any known server
logger.warning(
f"SKIPPING Nº{values[i]} from {dl_start} to {end} !!")
logger.info('Reading data...')
data = TimeSeriesDict.read(save_file, channels)
logger.info('Starting PSD generation...')
f = data[channels[0]].crop(
start=to_gps(data[channels[0]].times[-1]) - LIGOTimeGPS(60),
end=to_gps(data[channels[0]].times[-1])).psd().frequencies
d = (to_gps(labels.times[-1]).seconds - to_gps(labels.times[1]).seconds)
for i, cluster in enumerate(clusters):
try:
psds = {
channel: FrequencySeries.read(filename, f'{cluster}-{channel}')
for channel in channels
}
logger.info(f'Loaded Nº{cluster}.')
except KeyError:
logger.info(
f'Doing Nº{cluster} ({100 * cluster_counts[i] / len(labels.value):.2f}% of data)...'
)
with Progress(f'psd Nº{cluster} ({i + 1}/{len(clusters)})',
len(channels) * d) as progress:
psds = {
channel: FrequencySeries(median(stack([
progress(data[channel].crop,
pc * d + (to_gps(time).seconds -
to_gps(labels.times[1]).seconds),
start=to_gps(time) - LIGOTimeGPS(60),
end=to_gps(time)).psd().value
for c, time in zip(labels.value, labels.times)
if c == cluster
]),
axis=0),
frequencies=f,
name=f'{cluster}-{channel}')
for pc, channel in enumerate(channels)
}
for name in psds.keys():
psds[name].write(filename, **writing_opts)
# plotting is slow, so show a nice progress bar.
logger.debug('Initiating plotting routine...')
with Progress('plotting', len(groups)) as progress:
for p, (group, lbls, title) in enumerate(groups):
# plot the group in one figure.
plt = Plot(*(psds[channel] for channel in group),
separate=False,
sharex=True,
zorder=1,
**kwargs)
# plt.gca().set_xlim((30,60))
# modify the figure as a whole.
# plt.add_segments_bar(dq, label='')
plt.gca().set_xscale('log')
plt.gca().set_yscale('log')
plt.suptitle(title)
plt.legend(lbls)
# save to png.
progress(
plt.save, p,
get_path(f'{cluster}-{title}',
'png',
prefix=f'{prefix}/{cluster}'))
def wait_error():
progress = Progress(20)
for i in range(21):
if i: progress.increment()
time.sleep(ERROR_TIME / 21.0)
progress.done()
def train(train_story,
train_questions,
train_qstory,
memory,
model,
loss,
general_config,
train_logger,
val_logger,
global_batch_iter=0,
best_val_cost=1000000.,
best_val_err=1000000.):
train_config = general_config.train_config
dictionary = general_config.dictionary
nepochs = general_config.nepochs
nhops = general_config.nhops
batch_size = general_config.batch_size
enable_time = general_config.enable_time
randomize_time = general_config.randomize_time
lrate_decay_step = general_config.lrate_decay_step
train_range = general_config.train_range # indices of training questions
val_range = general_config.val_range # indices of validation questions
train_len = len(train_range)
val_len = len(val_range)
display_inteval = general_config.display_inteval
params = {
"lrate": train_config["init_lrate"],
"max_grad_norm": train_config["max_grad_norm"]
}
if randomize_time > 0:
print('We use Random Noise (RN) ratio of %.1f' % randomize_time)
# train/val start
for ep in range(nepochs):
# Decrease learning rate after every decay step
if (ep + 1) % lrate_decay_step == 0:
params["lrate"] *= 0.5
total_err = 0.
total_cost = 0.
total_num = 0
batch_iter = 0
for _ in Progress(range(int(math.floor(train_len / batch_size)))):
# Question batch
batch = train_range[np.random.randint(train_len, size=batch_size)]
input_data = np.zeros((train_story.shape[0], batch_size),
np.float32) # words of training questions
target_data = train_questions[2,
batch] # indices of training answers
memory[0].data[:] = dictionary["nil"]
# Compose batch of training data
for b in range(batch_size):
# NOTE: +1 since train_questions[1, :] is the index of the sentence right before the training question.
# d is a batch of [word indices in sentence, sentence indices from batch] for this story
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]]
# Pick a fixed number of latest sentences (before the question) from the story
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:]
# Training data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d
if enable_time:
# Inject noise into time index (i.e. word index)
if randomize_time > 0:
# Random number of blank (must be < total sentences until the training question?)
nblank = np.random.randint(
int(math.ceil(d.shape[1] * randomize_time)))
rt = np.random.permutation(d.shape[1] + nblank)
rt[rt >= train_config["sz"]] = train_config[
"sz"] - 1 # put the cap
# Add random time (must be > dictionary's length) into the time word (decreasing order)
memory[0].data[-1, :d.shape[1], b] = np.sort(
rt[:d.shape[1]])[::-1] + len(dictionary)
else:
memory[0].data[-1, :d.shape[1], b] = \
np.arange(d.shape[1])[::-1] + len(dictionary)
input_data[:, b] = train_qstory[:, batch[b]]
for i in range(1, nhops):
memory[i].data = memory[0].data
out = model.fprop(input_data)
cost = loss.fprop(out, target_data)
err = loss.get_error(out, target_data)
total_cost += cost
total_err += err
total_num += batch_size
grad = loss.bprop(out, target_data)
model.bprop(input_data, grad)
model.update(params)
batch_iter += 1
global_batch_iter += 1
if batch_iter % display_inteval == 0:
print("%d | %d | %g | loss: %g | err: %g" %
(ep, global_batch_iter, params['lrate'],
cost / batch_size, err / batch_size))
sys.stdout.flush()
train_logger.write('%d %d %f %f %f\n' %
(ep, global_batch_iter, params['lrate'],
cost / batch_size, err / batch_size))
train_logger.flush()
for i in range(nhops):
memory[i].emb_query.weight.D[:, 0] = 0
# Validation
total_val_err = 0.
total_val_cost = 0.
total_val_num = 0
for k in range(int(math.floor(val_len / batch_size))):
batch = val_range[np.arange(k * batch_size, (k + 1) * batch_size)]
input_data = np.zeros((train_story.shape[0], batch_size),
np.float32)
target_data = train_questions[2, batch]
memory[0].data[:] = dictionary["nil"]
for b in range(batch_size):
d = train_story[:, :(1 + train_questions[1, batch[b]]),
train_questions[0, batch[b]]]
offset = max(0, d.shape[1] - train_config["sz"])
d = d[:, offset:]
# Data for the 1st memory cell
memory[0].data[:d.shape[0], :d.shape[1], b] = d
if enable_time:
memory[0].data[-1, :d.shape[1], b] = np.arange(
d.shape[1])[::-1] + len(dictionary)
input_data[:, b] = train_qstory[:, batch[b]]
for i in range(1, nhops):
memory[i].data = memory[0].data
out = model.fprop(input_data)
val_cost = loss.fprop(out, target_data)
val_err = loss.get_error(out, target_data)
total_val_cost += val_cost
total_val_err += val_err
total_val_num += batch_size
current_val_cost = total_val_cost / total_val_num
current_val_err = total_val_err / total_val_num
print("%d | %d | val loss: %g | val err: %g" %
(ep, global_batch_iter, current_val_cost, current_val_err))
sys.stdout.flush()
if best_val_cost > current_val_cost:
print('current: %f, best: %f' % (current_val_cost, best_val_cost))
best_model = model
best_memory = memory
best_val_cost = current_val_cost
best_val_err = current_val_err
print('Best val loss: %f, val err: %f' %
(best_val_cost, best_val_err))
sys.stdout.flush()
train_error = total_err / total_num
val_error = total_val_err / total_val_num
val_logger.write('%d %d %f %f %f\n' % \
(ep, global_batch_iter, params['lrate'], current_val_cost, current_val_err))
val_logger.flush()
return train_logger,\
val_logger,\
best_model,\
best_memory,\
global_batch_iter,\
best_val_cost,\
best_val_err
def compute_all(channels,
start,
stop,
history=timedelta(hours=2),
filename=DEFAULT_FILENAME,
**kwargs):
# set up duration (minute-trend data has dt=1min, so reject intervals not on the minute).
duration = (stop - start).total_seconds() / 60
assert (stop - start).total_seconds() / 60 == (stop -
start).total_seconds() // 60
duration = int(duration)
logger.info(
f'Clustering data from {start} to {stop} ({duration} minutes).')
# download data using TimeSeries.get(), including history of point at t0.
logger.debug(
f'Initiating download from {start} to {stop} with history={history}...'
)
dl = TimeSeriesDict.get(channels,
start=to_gps(start - history),
end=to_gps(stop))
logger.info(f'Downloaded from {start} to {stop} with history={history}.')
if exists('input.npy'):
input_data = np.load('input.npy')
logger.info('Loaded input matrix.')
else:
# generate input matrix of the form [sample1;...;sampleN] with sampleK = [feature1,...,featureN]
# for sklearn.cluster algorithms. This is the slow part of the function, so a progress bar is shown.
logger.debug(f'Initiating input matrix generation...')
with Progress('building input', (duration * 60)) as progress:
input_data = stack([
concatenate([
progress(dl[channel].crop,
t,
start=to_gps(start + timedelta(seconds=t) -
history),
end=to_gps(start + timedelta(seconds=t))).value
for channel in channels
]) for t in range(0, int(duration * 60), 60)
])
# verify input matrix dimensions.
assert input_data.shape == (duration,
int(
len(channels) *
history.total_seconds() / 60))
np.save('input.npy', input_data)
logger.info('Completed input matrix generation.')
params = {
'quantile': .3,
'eps': .3,
'damping': .9,
'preference': -200,
'n_neighbors': 10,
'n_clusters': 15,
'min_samples': 20,
'xi': 0.05,
'min_cluster_size': 0.1
}
if exists('X.npy'):
X = np.load('X.npy')
logger.info('Loaded X')
else:
# normalize dataset for easier parameter selection
X = StandardScaler().fit_transform(input_data)
np.save('X.npy', X)
logger.info('Generated X')
if exists('bandwidth.npy'):
bandwidth = np.load('bandwidth.npy')
logger.info('Loaded bandwidth')
else:
# estimate bandwidth for mean shift
bandwidth = cluster.estimate_bandwidth(X, quantile=params['quantile'])
np.save('bandwidth.npy', bandwidth)
logger.info('Generated bandwidth')
if exists('connectivity.npy'):
connectivity = np.load('connectivity.npy', allow_pickle=True)
logger.info('Loaded connectivity')
else:
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(X,
n_neighbors=params['n_neighbors'],
include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
np.save('connectivity.npy', connectivity)
logger.info('Generated connectivity')
ms = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
two_means = cluster.MiniBatchKMeans(n_clusters=params['n_clusters'])
ward = cluster.AgglomerativeClustering(n_clusters=params['n_clusters'],
linkage='ward',
connectivity=connectivity)
spectral = cluster.SpectralClustering(n_clusters=params['n_clusters'],
eigen_solver='arpack',
affinity="nearest_neighbors")
dbscan = cluster.DBSCAN(eps=params['eps'])
optics = cluster.OPTICS(min_samples=params['min_samples'],
xi=params['xi'],
min_cluster_size=params['min_cluster_size'])
affinity_propagation = cluster.AffinityPropagation(
damping=params['damping'], preference=params['preference'])
average_linkage = cluster.AgglomerativeClustering(
linkage="average",
affinity="cityblock",
n_clusters=params['n_clusters'],
connectivity=connectivity)
birch = cluster.Birch(n_clusters=params['n_clusters'])
gmm = mixture.GaussianMixture(n_components=params['n_clusters'],
covariance_type='full')
clustering_algorithms = (
('MiniBatchKMeans', two_means),
('AffinityPropagation', affinity_propagation), ('MeanShift', ms),
('SpectralClustering', spectral), ('DBSCAN', dbscan),
('OPTICS', optics), ('Birch', birch), ('GaussianMixture', gmm)
# ('Ward', ward),
# ('AgglomerativeClustering', average_linkage),
)
for name, algorithm in clustering_algorithms:
if exists(f'part-{name}-{filename}'):
labels = TimeSeries.read(f'part-{name}-{filename}',
f'{name}-labels')
logger.debug(f'LOADED {name}.')
else:
logger.debug(f'doing {name}...')
# catch warnings related to kneighbors_graph
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message="the number of connected components of the " +
"connectivity matrix is [0-9]{1,2}" +
" > 1. Completing it to avoid stopping the tree early.",
category=UserWarning)
warnings.filterwarnings(
"ignore",
message="Graph is not fully connected, spectral embedding"
+ " may not work as expected.",
category=UserWarning)
algorithm.fit(X)
if hasattr(algorithm, 'labels_'):
y_pred = algorithm.labels_.astype(np.int)
else:
y_pred = algorithm.predict(X)
# cast the output labels to a TimeSeries so that cropping is easy later on.
labels = TimeSeries(
y_pred,
times=dl[channels[0]].crop(start=to_gps(start),
end=to_gps(stop)).times,
name=f'{name}-labels')
labels.write(f'part-{name}-{filename}')
# put labels in data download dictionary for easy saving.
dl[labels.name] = labels
# write data download and labels to specified filename.
cache_file = abspath(filename)
if exists(cache_file):
remove(cache_file)
dl.write(cache_file)
logger.info(f'Wrote cache to {filename}')