def __init__(self, url, timeout=30, utxo_cache=False, debug=False):
self.sessionmaker = sessionmaker(bind=create_engine(url, connect_args={'connect_timeout': timeout}, encoding='utf8', echo=debug))
self.address_cache = LFUCache(maxsize=16384)
self.txid_cache = RRCache(maxsize=131072)
self.utxo_cache = RRCache(maxsize=262144) if utxo_cache else None
super(DatabaseIO, self).__init__(self.sessionmaker(), address_cache=self.address_cache, txid_cache=self.txid_cache, utxo_cache=self.utxo_cache)
def __init__(self, raw_slices, pmap_slices, gt_slices, patch_radius, batch_size, cache_size=5,
p_from_cache=0.97):
self.raw_slices = raw_slices
self.pmap_slices = pmap_slices
self.gt_slices = gt_slices
self.patch_radius = patch_radius
self.batch_size = batch_size
self.n_slices = raw_slices.shape[0]
self.cache = RRCache(maxsize=cache_size)
self.p_from_cache = p_from_cache
def get_cache(cache_type, cache_size):
caches = {
'lfu': LFUCache(cache_size),
'lru': LRUCache(cache_size),
#'rl' : RLCache(cache_size),
'rr': RRCache(cache_size)
}
try:
return caches[cache_type]
except KeyError:
return default()
class MEGSexDataset(MEGDataset, BaseDatasetSex):
LOAD_SUFFIX = '.npy'
cache = RRCache(10000)
# Do not cache the raw data
@staticmethod
@cached(cache)
def get_features(path_to_file):
return np.load(path_to_file[0])
@property
def modality_folders(self):
return ['raw/MEG']
def main():
cache_size = 5
data_size = 100
num_accesses = 10000
std_dev = 3
accesses, data = init(data_size, num_accesses, std_dev)
cache = OPTCache(cache_size, accesses)
optimal_hits, optimal_misses = run(cache, accesses, data)
cache = RRCache(cache_size)
cache_hits, cache_misses = run(cache, accesses, data)
print(optimal_hits, optimal_misses)
print(cache_hits, cache_misses)
class MEGRawRanges(MEGAgeRangesDataset):
LOAD_SUFFIX = '.npy'
cache = RRCache(10000)
# Do not cache the raw data
@staticmethod
@cached(cache)
def get_features(path_to_file):
return np.load(path_to_file[0])
@property
def modality_folders(self):
return ['raw/MEG']
def inputshape(self):
# FIXME should not have magic number, comes from assumed sample rate of 200
return 700, self.slice_length
def test_rr(self):
cache = RRCache(maxsize=2, choice=min)
self.assertEqual(min, cache.choice)
cache[1] = 1
cache[2] = 2
cache[3] = 3
self.assertEqual(2, len(cache))
self.assertEqual(2, cache[2])
self.assertEqual(3, cache[3])
self.assertNotIn(1, cache)
cache[0] = 0
self.assertEqual(2, len(cache))
self.assertEqual(0, cache[0])
self.assertEqual(3, cache[3])
self.assertNotIn(2, cache)
cache[4] = 4
self.assertEqual(2, len(cache))
self.assertEqual(3, cache[3])
self.assertEqual(4, cache[4])
self.assertNotIn(0, cache)
import random
import numpy as np
import synth
from target import GENE_LABELS, GENE_VALUES
from deap import creator, base, tools
import librosa
from cachetools import cached, RRCache
from cachetools.keys import hashkey
# Define experiment settings
sr = 44100
cache = RRCache(maxsize=100)
def individual_to_params(individual):
"""
Converts an individual to a dictionary of parameter values
"""
return dict(zip(GENE_LABELS, individual))
def extract_features(sound_array):
"""
Extracts MFCC and spectral bandwidth, centroid, flatness, and roll-off
It seems that only MFCC features already perform quite well
"""
return librosa.feature.mfcc(sound_array, sr).flatten()
@cached(cache,
key=lambda individual, target_features: hashkey(
def cache(self, maxsize, choice=choice, missing=None, getsizeof=None):
return RRCache(maxsize, choice=choice, missing=missing,
getsizeof=getsizeof)
class BaseDataset:
DATASET_TARGETS = [HEADER_AGE]
NUM_BUCKETS = 5
LOAD_SUFFIX = '.npy'
# Not sure I like this...
GENERATOR = SubjectFileLoader
cache = RRCache(2 * 16384)
@staticmethod
# @lru_cache(maxsize=8192)
@cached(cache)
def get_features(path_to_file):
"""
Loads arrays from file, and returned as a flattened vector, cached to save some time
:param path_to_file:
:return: numpy vector
"""
# return loadmat(path_to_file, squeeze_me=True)['features'].ravel()
l = np.load(path_to_file[0])
#
# if self.megind is not None:
# l = l[:, self.megind].squeeze()
# l = zscore(l)
return l
@staticmethod
def print_folds(buckets):
for i, b in enumerate(buckets):
b = np.array(b)
print('Fold {0}, total datapoints: {1}'.format(i + 1, b.shape[0]))
subjects, counts = np.unique(b[:, 0], return_counts=True)
print('{0} Subjects used: {1}\nPoints per subject: {2}\n\n'.format(
len(subjects), subjects, counts))
def __init__(self,
toplevel,
PDK=True,
PA=True,
VG=True,
MO=False,
batchsize=2):
self.toplevel = Path(toplevel)
# some basic checking to make sure we have the right directory
if not self.toplevel.exists() or not self.toplevel.is_dir():
raise NotADirectoryError(
"Provided top level directory is not directory")
self.subject_hash = parsesubjects(self.toplevel / SUBJECT_STRUCT)
self.batchsize = batchsize
self.traindata = None
tests = []
# Assemble which experiments we are going to be using
if PDK:
tests.append(TEST_PDK)
if PA:
tests.append(TEST_PA)
if VG:
tests.append(TEST_VG)
if MO:
tests.append(TEST_MO)
if self.preprocessed_file in [
x.name for x in self.toplevel.iterdir() if not x.is_dir()
]:
with (self.toplevel / self.preprocessed_file).open('rb') as f:
print('Loaded previous preprocessing!')
self.buckets, self.longest_vector, self.slice_length,\
self.testpoints, self.training_subjects = pickle.load(f)
# list of subjects that we will use for the cross validation
# self.leaveoutsubjects = np.unique(self.datapoints[:, 0])
# Todo: warn/update pickled file if new subjects exist
self.print_folds(self.buckets)
else:
print('Preprocessing data...')
self.training_subjects, self.longest_vector, self.slice_length = self.files_to_load(
tests)
if TEST_SUBJECTS:
print('Forcing test subjects...')
testsubjects = TEST_SUBJECTS
else:
testsubjects = np.random.choice(
list(self.training_subjects.keys()),
int(len(self.training_subjects) / 10),
replace=False)
self.testpoints = np.array([
item for x in testsubjects
for item in self.training_subjects[x]
])
for subject in testsubjects:
self.training_subjects.pop(subject)
print('Subjects used for testing:', testsubjects)
datapoint_ordering = sorted(
self.training_subjects,
key=lambda x: -len(self.training_subjects[x]))
self.buckets = [[] for x in range(self.NUM_BUCKETS)]
# Fill the buckets up and down
for i in range(len(datapoint_ordering)):
if int(i / self.NUM_BUCKETS) % 2:
index = self.NUM_BUCKETS - (i % self.NUM_BUCKETS) - 1
self.buckets[int(index)].extend(
self.training_subjects[datapoint_ordering[i]])
else:
self.buckets[int(i % self.NUM_BUCKETS)].extend(
self.training_subjects[datapoint_ordering[i]])
with (self.toplevel / self.preprocessed_file).open('wb') as f:
pickle.dump(
(self.buckets, self.longest_vector, self.slice_length,
self.testpoints, self.training_subjects), f)
# numpoints = self.datapoints.size[0]
# ind = np.arange(numpoints)
# ind = np.random.choice(ind, replace=False, size=int(0.2*numpoints)
self.print_folds(self.buckets)
self.next_leaveout(force=0)
@property
@abstractmethod
def modality_folders(self) -> list:
"""
Subclasses must implement this so that it reports the name of the folder(s) to find experiments, once in the
subject folder.
:return:
"""
pass
def files_to_load(self, tests):
"""
This should be implemented by subclasses to specify what files
:param tests: The type of tests that should make up the dataset
:return: A dictionary for the loaded subjects
:rtype: tuple
"""
longest_vector = -1
slice_length = -1
loaded_subjects = {}
for subject in tqdm([
x for x in self.toplevel.iterdir()
if x.is_dir() and x.name in self.subject_hash.keys()
]):
tqdm.write('Loading subject ' + subject.stem + '...')
loaded_subjects[subject.stem] = []
for experiment in tqdm([
t for e in self.modality_folders if (subject / e).exists()
for t in (subject / e).iterdir() if t.name in tests
]):
for epoch in tqdm([
l for l in experiment.iterdir()
if l.suffix == self.LOAD_SUFFIX
]):
try:
# f = loadmat(str(epoch), squeeze_me=True)
f = self.get_features(tuple([epoch]))
if np.isnan(f).any():
tqdm.write('NaNs found in ' + str(epoch))
time.sleep(1)
# slice_length = max(slice_length, len(f['header']))
# longest_vector = max(longest_vector,
# len(f['features'].reshape(-1)))
slice_length = max(slice_length, f.shape[1])
longest_vector = max(longest_vector,
f.shape[0] * f.shape[1])
loaded_subjects[subject.stem].append(
(subject.stem, epoch))
except Exception as e:
tqdm.write(
'Warning: Skipping file, error occurred loading: '
+ str(epoch))
return loaded_subjects, longest_vector, slice_length
@property
@abstractmethod
def preprocessed_file(self):
pass
def next_leaveout(self, force=None):
"""
Moves on to the next group to leaveout.
:return: Number of which leaveout, `None` if complete
"""
if force is not None:
self.leaveout = force
if self.leaveout == self.NUM_BUCKETS:
print('Have completed cross-validation')
self.leaveout = None
# raise CrossValidationComplete
return self.leaveout
# Select next bucket to leave out as evaluation
self.eval_points = np.array(self.buckets[self.leaveout])
# Convert the remaining buckets into one list
self.traindata = np.array([
item for sublist in self.buckets for item in sublist
if self.buckets.index(sublist) != self.leaveout
])
self.leaveout += 1
return self.leaveout
def current_leaveout(self):
return self.leaveout
def sanityset(self, fold=3, batchsize=None, flatten=True):
"""
Provides a generator for a small subset of data to ensure that the model can train to it
:return:
"""
if batchsize is None:
batchsize = self.batchsize
return self.GENERATOR(np.array(
self.buckets[fold]
[int(0 * len(self.buckets[fold])):int(1 *
len(self.buckets[fold]))]),
self.toplevel,
self.longest_vector,
self.subject_hash,
self.DATASET_TARGETS,
self.slice_length,
self.get_features,
batchsize=batchsize,
flatten=flatten)
def trainingset(self, batchsize=None, flatten=True):
"""
Provides a generator object with the current training set
:param flatten: Whether to flatten the resulting
:param batchsize:
:return: Generator of type :class`.SubjectFileLoader`
"""
if batchsize is None:
batchsize = self.batchsize
if self.traindata is None:
raise AttributeError(
'No fold initialized... Try calling next_leaveout')
return self.GENERATOR(self.traindata,
self.toplevel,
self.longest_vector,
self.subject_hash,
self.DATASET_TARGETS,
self.slice_length,
self.get_features,
batchsize=batchsize,
flatten=flatten)
def evaluationset(self, batchsize=None, flatten=True):
"""
Provides a generator object with the current training set
:param batchsize:
:return: Generator of type :class`.SubjectFileLoader`
"""
if batchsize is None:
batchsize = self.batchsize
return self.GENERATOR(self.eval_points,
self.toplevel,
self.longest_vector,
self.subject_hash,
self.DATASET_TARGETS,
self.slice_length,
self.get_features,
batchsize=batchsize,
flatten=flatten,
evaluate=True)
def testset(self, batchsize=None, flatten=True):
"""
Provides a generator object with the current training set
:param batchsize:
:return: Generator of type :class`.SubjectFileLoader`
"""
if batchsize is None:
batchsize = self.batchsize
return self.GENERATOR(self.testpoints,
self.toplevel,
self.longest_vector,
self.subject_hash,
self.DATASET_TARGETS,
self.slice_length,
self.get_features,
batchsize=batchsize,
flatten=flatten,
evaluate=True)
def inputshape(self):
return int(self.longest_vector // self.slice_length), self.slice_length
def outputshape(self):
return len(self.DATASET_TARGETS)
class IsbiJ3Feeder(object):
def __init__(self, raw_slices, pmap_slices, gt_slices, patch_radius, batch_size, cache_size=5,
p_from_cache=0.97):
self.raw_slices = raw_slices
self.pmap_slices = pmap_slices
self.gt_slices = gt_slices
self.patch_radius = patch_radius
self.batch_size = batch_size
self.n_slices = raw_slices.shape[0]
self.cache = RRCache(maxsize=cache_size)
self.p_from_cache = p_from_cache
def __call__(self):
batch_images = [None]*self.batch_size
batch_gt = [None]*self.batch_size
batch_gt_quali = [None]*self.batch_size
for i in range(self.batch_size):
# get a patch extractor
patch_extractor = self.__get_random_slice_data()
# get a random 0-cell index
# but we only consider 0-cells with
# a since of 3
n_patches = len(patch_extractor)
j3_labels = patch_extractor.j3_labels
assert len(j3_labels) >=1
done = False
while(not done):
rand_index = random.randint(0, len(j3_labels)-1)
cell_0_label = j3_labels[rand_index]
assert cell_0_label >= 1
cell_0_index = cell_0_label - 1
try:
done = True
img, gt, gt_quali = patch_extractor[cell_0_index]
except:
print("hubs....")
done = False
# img shape atm : x,y,c
# => desired 1,c,x,y
img = numpy.rollaxis(img, 2,0)[None,...]
batch_images[i] = img
batch_gt[i] = gt
batch_gt_quali[i] = gt_quali
batch_images = numpy.concatenate(batch_images,axis=0)
#print("batch_gt",batch_gt)
batch_gt = numpy.array(batch_gt)
batch_gt_quali = numpy.array(batch_gt_quali)
# batch_images: (batch_size, c, x,y)
# batch_gt: (batch_size, 3)
return batch_images, batch_gt, batch_gt_quali
def __get_random_slice_data(self):
take_from_cache = random.random() >= (1.0 - self.p_from_cache )
if take_from_cache and len(self.cache)>0:
# get random item from cache via pop
# (since this is a random cache this
# will lead to a random item)
per_slice_data = self.__get_random_from_cache()
return per_slice_data
else:
# (maybe) compute new
# random slice
slice_index = random.randint(0, self.n_slices-1)
# get the per_slice_data from cache iff already in cache.
# Iff not in cache, compute per_slice_data and put to cache
per_slice_data = self.__force_to_cache(slice_index=slice_index)
return per_slice_data
def __get_random_from_cache(self):
assert len(self.cache) > 0
slice_index, per_slice_data = self.cache.popitem()
self.cache[slice_index] = per_slice_data
return per_slice_data
def __force_to_cache(self, slice_index):
if slice_index in self.cache:
per_slice_data = self.cache[slice_index]
return per_slice_data
else:
per_slice_data = self.__compute_per_slice_data(slice_index)
self.cache[slice_index] = per_slice_data
return per_slice_data
def __edge_gt_to_node_gt(self, edge_gt):
# the edge_gt is on membrane level
# 0 at membranes pixels
# 1 at non-membrane piper_slice_dataxels
seeds = nifty.segmentation.localMaximaSeeds(edge_gt)
growMap = nifty.filters.gaussianSmoothing(1.0-edge_gt, 1.0)
growMap += 0.1*nifty.filters.gaussianSmoothing(1.0-edge_gt, 6.0)
gt = nifty.segmentation.seededWatersheds(growMap, seeds=seeds)
return gt
def __compute_per_slice_data(self, slice_index):
raw_slice = self.raw_slices[slice_index,:,:]
gt_slice = self.gt_slices[slice_index,:,:]
pmap_slice = self.pmap_slices[slice_index,:,:]
edge_gt = self.gt_slices[slice_index,:,:]
node_gt = self.__edge_gt_to_node_gt(edge_gt)
# randomized overseg
threshold = random.uniform(0.275, 0.55)
overseg = nifty.segmentation.distanceTransformWatersheds(pmap_slice.copy(),
threshold=threshold)
hl_cgp = HlCgp(overseg)
cell_0_patch_extrator = Cell0PatchExtrator(hl_cgp, image=raw_slice,
node_gt=node_gt,
radius=self.patch_radius)
return cell_0_patch_extrator
def __init__(self, max_dim):
"""
:param max_dim:
"""
self.cache = RRCache(maxsize=max_dim)
class CoapRRCache(CoapCache):
def __init__(self, max_dim):
"""
:param max_dim:
"""
self.cache = RRCache(maxsize=max_dim)
def update(self, key, element):
"""
:param key:
:param element:
:return:
"""
print "updating cache"
print "key: ", key.hashkey
print "element: ", element
self.cache.update([(key.hashkey, element)])
def get(self, key):
"""
:param key:
:return: CacheElement
"""
try:
print "Getting cache response"
response = self.cache[key.hashkey]
except KeyError:
print "problem here"
response = None
return response
def is_full(self):
"""
:return:
"""
if self.cache.currsize == self.cache.maxsize:
return True
return False
def is_empty(self):
"""
:return:
"""
if self.cache.currsize == 0:
return True
return False
def debug_print(self):
"""
:return:
"""
print "size = ", self.cache.currsize
list = self.cache.items()
for key, element in list:
print "element.max age ", element.max_age
print "element.uri", element.uri
print "element.freshness ", element.freshness
