def take_slice_of_analogsignalarray_by_channelindex(self,
channel_indexes=None):
'''
Return slices of the :class:`AnalogSignalArrays` in the
:class:`Segment` that correspond to the :attr:`channel_indexes`
provided.
'''
if channel_indexes is None:
return []
sliced_sigarrays = []
for sigarr in self.analogsignals:
if sigarr.get_channel_index() is not None:
ind = np.in1d(sigarr.get_channel_index(), channel_indexes)
sliced_sigarrays.append(sigarr[:, ind])
return sliced_sigarrays
python类in1d()的实例源码
def take_slice_of_analogsignalarray_by_channelindex(self,
channel_indexes=None):
'''
Return slices of the :class:`AnalogSignalArrays` in the
:class:`Segment` that correspond to the :attr:`channel_indexes`
provided.
'''
if channel_indexes is None:
return []
sliced_sigarrays = []
for sigarr in self.analogsignals:
if sigarr.get_channel_index() is not None:
ind = np.in1d(sigarr.get_channel_index(), channel_indexes)
sliced_sigarrays.append(sigarr[:, ind])
return sliced_sigarrays
def get_1000G_snps(sumstats, out_file):
sf = np.loadtxt(sumstats,dtype=str,skiprows=1)
h5f = h5py.File('ref/Misc/1000G_SNP_info.h5','r')
rf = h5f['snp_chr'][:]
h5f.close()
ind1 = np.in1d(sf[:,1],rf[:,2])
ind2 = np.in1d(rf[:,2],sf[:,1])
sf1 = sf[ind1]
rf1 = rf[ind2]
### check order ###
if sum(sf1[:,1]==rf1[:,2])==len(rf1[:,2]):
print 'Good!'
else:
print 'Shit happens, sorting sf1 to have the same order as rf1'
O1 = np.argsort(sf1[:,1])
O2 = np.argsort(rf1[:,2])
O3 = np.argsort(O2)
sf1 = sf1[O1][O3]
out = ['hg19chrc snpid a1 a2 bp or p'+'\n']
for i in range(len(sf1[:,1])):
out.append(sf1[:,0][i]+' '+sf1[:,1][i]+' '+sf1[:,2][i]+' '+sf1[:,3][i]+' '+rf1[:,1][i]+' '+sf1[:,5][i]+' '+sf1[:,6][i]+'\n')
ff = open(out_file,"w")
ff.writelines(out)
ff.close()
def test_multicollinearity(df, target_name, r2_threshold = 0.89):
'''Tests if any of the features could be predicted from others with R2 >= 0.89
input: dataframe, name of target (to exclude)
'''
r2s = pd.DataFrame()
for feature in df.columns.difference([target_name]):
model = sk.linear_model.Ridge()
model.fit(df[df.columns.difference([target_name,feature])], df[feature])
pos = np.in1d(model.coef_, np.sort(model.coef_)[-5:])
r2s = r2s.append(pd.DataFrame({'r2':sk.metrics.r2_score(df[feature],\
model.predict(df[df.columns.difference([target_name, feature])])),\
'predictors' : str(df.columns.difference([target_name, feature])[np.ravel(np.argwhere(pos == True))].tolist())}, index = [feature]))
print('Testing', feature)
print('-----------------')
if len(r2s[r2s['r2'] >= r2_threshold]) > 0:
print('Multicollinearity detected')
print(r2s[r2s['r2'] >= r2_threshold])
else:
print('No multicollinearity')
def __init__(self, **kwargs):
logging.info('Crossword __init__: Initializing crossword...')
logging.debug('kwargs:', kwargs)
# Reading kwargs
self.setup = kwargs
self.rows = int(kwargs.get('n', 5))
self.cols = int(kwargs.get('m', 5))
self.words_file = str(kwargs.get('word_file', 'lemma.num.txt'))
self.sort = bool(kwargs.get('sort', False))
self.maximize_len = bool(kwargs.get('maximize_len', False))
self.repeat_words = bool(kwargs.get('repeat_words', False))
logging.debug('Crossword __init__: n={}, m={}, fname={}'.format(self.rows, self.cols, self.words_file))
# Loading words
logging.debug('Crossword __init__: Started loading words from {}'.format(self.words_file))
arr = np.genfromtxt(self.words_file, dtype='str', delimiter=' ')
self.words = arr[np.in1d(arr[:, 3], ['v', 'n', 'adv', 'a'])][:, 2].tolist()
# Number of words loaded
logging.debug('Crossword __init__: Number of words loaded: {}'.format(len(self.words)))
self.words = list(set(x for x in self.words if len(x) <= self.rows and len(x) <= self.cols))
if self.sort:
self.words = sorted(self.words, key=len, reverse=self.maximize_len)
# After filter logging
logging.debug('Crossword __init__: Number of words after filter: {}, maxlen = {}'.format(len(self.words), len(
max(self.words, key=len))))
def test_df_col_or_idx_equivalence(df1,
df2,
col=None):
'''check whether two dataframes contain the same elements (but not
necessarily in the same order) in either the indexes or a selected column
inputs
df1, df2
the dataframes to check
col
if not None, test this dataframe column for equivalency, otherwise
test the dataframe indexes
Returns True or False
'''
if not col:
result = all(np.in1d(df1.index, df2.index,
assume_unique=True,
invert=False))
else:
result = all(np.in1d(df1[col], df2[col],
assume_unique=False,
invert=False))
return result
def make_classifier(self, name, ids, labels):
"""Entrenar un clasificador SVM sobre los textos cargados.
Crea un clasificador que se guarda en el objeto bajo el nombre `name`.
Args:
name (str): Nombre para el clasidicador.
ids (list): Se espera una lista de N ids de textos ya almacenados
en el TextClassifier.
labels (list): Se espera una lista de N etiquetas. Una por cada id
de texto presente en ids.
Nota:
Usa el clasificador de `Scikit-learn <http://scikit-learn.org/>`_
"""
if not all(np.in1d(ids, self.ids)):
raise ValueError("Hay ids de textos que no se encuentran \
almacenados.")
setattr(self, name, SGDClassifier())
classifier = getattr(self, name)
indices = np.searchsorted(self.ids, ids)
classifier.fit(self.tfidf_mat[indices, :], labels)
def retrain(self, name, ids, labels):
"""Reentrenar parcialmente un clasificador SVM.
Args:
name (str): Nombre para el clasidicador.
ids (list): Se espera una lista de N ids de textos ya almacenados
en el TextClassifier.
labels (list): Se espera una lista de N etiquetas. Una por cada id
de texto presente en ids.
Nota:
Usa el clasificador de `Scikit-learn <http://scikit-learn.org/>`_
"""
if not all(np.in1d(ids, self.ids)):
raise ValueError("Hay ids de textos que no se encuentran \
almacenados.")
try:
classifier = getattr(self, name)
except AttributeError:
raise AttributeError("No hay ningun clasificador con ese nombre.")
indices = np.in1d(self.ids, ids)
if isinstance(labels, str):
labels = [labels]
classifier.partial_fit(self.tfidf_mat[indices, :], labels)
def get_feedback_data(self, on_level=None):
feedback = self.data.fields.feedback
eval_data = self.data.test.evalset[feedback].values
holdout = self.data.holdout_size
feedback_data = eval_data.reshape(-1, holdout)
if on_level is not None:
try:
iter(on_level)
except TypeError:
feedback_data = np.ma.masked_not_equal(feedback_data, on_level)
else:
mask_level = np.in1d(feedback_data.ravel(),
on_level,
invert=True).reshape(feedback_data.shape)
feedback_data = np.ma.masked_where(mask_level, feedback_data)
return feedback_data
def _find_optimal_clustering(self,clusterings):
max_score = float('-inf')
max_clustering = None
for clustering in clusterings:
labeled_vectors = [(node.vector,cluster_idx) for cluster_idx in range(len(clustering)) for node in _get_cluster_nodes(clustering[cluster_idx][1]) ]
vectors,labels = [np.array(x) for x in zip(*labeled_vectors)]
if np.in1d([1],labels)[0]:
score = silhouette_score(vectors,labels,metric='cosine')
else:
continue # silhouette doesn't work with just one cluster
if score > max_score:
max_score = score
max_clustering = clustering
return zip(*max_clustering)[1] if max_clustering else zip(*clusterings[0])[1]
def remove_rare_elements(data, min_user_activity, min_item_popularity):
'''Removes user and items that appears in too few interactions.
min_user_activity is the minimum number of interaction that a user should have.
min_item_popularity is the minimum number of interaction that an item should have.
NB: the constraint on item might not be strictly satisfied because rare users and items are removed in alternance,
and the last removal of inactive users might create new rare items.
'''
print('Remove inactive users and rare items...')
#Remove inactive users a first time
user_activity = data.groupby('u').size()
data = data[np.in1d(data.u, user_activity[user_activity >= min_user_activity].index)]
#Remove unpopular items
item_popularity = data.groupby('i').size()
data = data[np.in1d(data.i, item_popularity[item_popularity >= min_item_popularity].index)]
#Remove users that might have passed below the activity threshold due to the removal of rare items
user_activity = data.groupby('u').size()
data = data[np.in1d(data.u, user_activity[user_activity >= min_user_activity].index)]
return data
def reconstruct_goal(world):
# pdb.set_trace()
world = world.copy()
## indices for grass and puddle
background_inds = [obj['index'] for (name, obj) in library.objects.iteritems() if obj['background']]
## background mask
background = np.in1d(world, background_inds)
background = background.reshape( (world.shape) )
## set backgronud to 0
world[background] = 0
## subtract largest background ind
## so indices of objects begin at 1
world[~background] -= max(background_inds)
world = np.expand_dims(np.expand_dims(world, 0), 0)
# pdb.set_trace()
return world
def check_multiplication_dims(dims, N, M, vidx=False, without=False):
dims = array(dims, ndmin=1)
if len(dims) == 0:
dims = arange(N)
if without:
dims = setdiff1d(range(N), dims)
if not np.in1d(dims, arange(N)).all():
raise ValueError('Invalid dimensions')
P = len(dims)
sidx = np.argsort(dims)
sdims = dims[sidx]
if vidx:
if M > N:
raise ValueError('More multiplicants than dimensions')
if M != N and M != P:
raise ValueError('Invalid number of multiplicants')
if P == M:
vidx = sidx
else:
vidx = sdims
return sdims, vidx
else:
return sdims
def particle_mask(self):
# Dynamically create the masking array for particles, and get
# the data using standard yt methods.
if self._particle_mask is not None:
return self._particle_mask
# This is from disk.
pid = self.__getitem__('particle_index')
# This is from the sphere.
if self._name == "RockstarHalo":
ds = self.ds.sphere(self.CoM, self._radjust * self.max_radius)
elif self._name == "LoadedHalo":
ds = self.ds.sphere(self.CoM, np.maximum(self._radjust * \
self.ds.quan(self.max_radius, 'code_length'), \
self.ds.index.get_smallest_dx()))
sp_pid = ds['particle_index']
self._ds_sort = sp_pid.argsort()
sp_pid = sp_pid[self._ds_sort]
# This matches them up.
self._particle_mask = np.in1d(sp_pid, pid)
return self._particle_mask
def has_approx_support(m, m_hat, prob=0.01):
"""Returns 1 if model selection error is less than or equal to prob rate,
0 else.
NOTE: why does np.nonzero/np.flatnonzero create so much problems?
"""
m_nz = np.flatnonzero(np.triu(m, 1))
m_hat_nz = np.flatnonzero(np.triu(m_hat, 1))
upper_diagonal_mask = np.flatnonzero(np.triu(np.ones(m.shape), 1))
not_m_nz = np.setdiff1d(upper_diagonal_mask, m_nz)
intersection = np.in1d(m_hat_nz, m_nz) # true positives
not_intersection = np.in1d(m_hat_nz, not_m_nz) # false positives
true_positive_rate = 0.0
if len(m_nz):
true_positive_rate = 1. * np.sum(intersection) / len(m_nz)
true_negative_rate = 1. - true_positive_rate
false_positive_rate = 0.0
if len(not_m_nz):
false_positive_rate = 1. * np.sum(not_intersection) / len(not_m_nz)
return int(np.less_equal(true_negative_rate + false_positive_rate, prob))
def get_membership_mask(self, labels, rows_or_columns):
from .util import array_tostring
assert rows_or_columns in ['rows', 'columns']
assert isinstance(labels, np.ndarray)
assert labels.size > 0
if rows_or_columns == "rows":
filter_labels = self.rowlabels
else:
filter_labels = self.columnlabels
labels = array_tostring(labels)
filter_labels = array_tostring(filter_labels)
return np.in1d(filter_labels.ravel(),
labels).reshape(filter_labels.shape)
def discrete(self, x, bin=5):
#res = np.array([0] * x.shape[-1], dtype=int)
#?????????????????????WOE?????????????<=?WOE??
x_copy = pd.Series.copy(x)
x_copy = x_copy.astype(str)
#x_copy = x_copy.astype(np.str_)
#x_copy = x
x_gt0 = x[x>=0]
#if x.name == 'TD_PLTF_CNT_1M':
#bin = 5
#x_gt0 = x[(x>=0) & (x<=24)]
for i in range(bin):
point1 = stats.scoreatpercentile(x_gt0, i * (100.0/bin))
point2 = stats.scoreatpercentile(x_gt0, (i + 1) * (100.0/bin))
x1 = x[(x >= point1) & (x <= point2)]
mask = np.in1d(x, x1)
#x_copy[mask] = i + 1
x_copy[mask] = '%s-%s' % (point1,point2)
#x_copy[mask] = point1
#print x_copy[mask]
#print x
#print x
return x_copy
def grade(self, x, bin=5):
#res = np.array([0] * x.shape[-1], dtype=int)
#?????????????????????WOE?????????????<=?WOE??
x_copy = np.copy(x)
#x_copy = x_copy.astype(str)
#x_copy = x_copy.astype(np.str_)
#x_copy = x
x_gt0 = x[x>=0]
for i in range(bin):
point1 = stats.scoreatpercentile(x_gt0, i * (100.0/bin))
point2 = stats.scoreatpercentile(x_gt0, (i + 1) * (100.0/bin))
x1 = x[(x >= point1) & (x <= point2)]
mask = np.in1d(x, x1)
#x_copy[mask] = i + 1
x_copy[mask] = i + 1
#x_copy[mask] = point1
#print x_copy[mask]
#print x
print point1,point2
#print x
return x_copy
def map_values(values, pos, target_pos, dtype=None, nan=dat.CPG_NAN):
"""Maps `values` array at positions `pos` to `target_pos`.
Inserts `nan` for uncovered positions.
"""
assert len(values) == len(pos)
assert np.all(pos == np.sort(pos))
assert np.all(target_pos == np.sort(target_pos))
values = values.ravel()
pos = pos.ravel()
target_pos = target_pos.ravel()
idx = np.in1d(pos, target_pos)
pos = pos[idx]
values = values[idx]
if not dtype:
dtype = values.dtype
target_values = np.empty(len(target_pos), dtype=dtype)
target_values.fill(nan)
idx = np.in1d(target_pos, pos).nonzero()[0]
assert len(idx) == len(values)
assert np.all(target_pos[idx] == pos)
target_values[idx] = values
return target_values
def test_learn_codes():
"""Test learning of codes."""
thresh = 0.25
X, ds, z = simulate_data(n_trials, n_times, n_times_atom, n_atoms)
for solver in ('l_bfgs', 'ista', 'fista'):
z_hat = update_z(X, ds, reg, n_times_atom, solver=solver,
solver_kwargs=dict(factr=1e11, max_iter=50))
X_hat = construct_X(z_hat, ds)
assert_true(np.corrcoef(X.ravel(), X_hat.ravel())[1, 1] > 0.99)
assert_true(np.max(X - X_hat) < 0.1)
# Find position of non-zero entries
idx = np.ravel_multi_index(z[0].nonzero(), z[0].shape)
loc_x, loc_y = np.where(z_hat[0] > thresh)
# shift position by half the length of atom
idx_hat = np.ravel_multi_index((loc_x, loc_y), z_hat[0].shape)
# make sure that the positions are a subset of the positions
# in the original z
mask = np.in1d(idx_hat, idx)
assert_equal(np.sum(mask), len(mask))
def __init__(self, topology, selstr=None, deg=False, cossin=False, periodic=True):
indices = indices_phi(topology)
if not selstr:
self._phi_inds = indices
else:
self._phi_inds = indices[np.in1d(indices[:, 1],
topology.select(selstr), assume_unique=True)]
indices = indices_psi(topology)
if not selstr:
self._psi_inds = indices
else:
self._psi_inds = indices[np.in1d(indices[:, 1],
topology.select(selstr), assume_unique=True)]
# alternate phi, psi pairs (phi_1, psi_1, ..., phi_n, psi_n)
dih_indexes = np.array(list(phi_psi for phi_psi in
zip(self._phi_inds, self._psi_inds))).reshape(-1, 4)
super(BackboneTorsionFeature, self).__init__(topology, dih_indexes,
deg=deg, cossin=cossin,
periodic=periodic)
def test_ttv_array_like_data_source(self):
dummy_data_source = DummyDataSource()
subject_info_dir = os.path.join('test', 'dummy_data', 'metadata')
ttv = yaml_to_dict(os.path.join(subject_info_dir, 'dummy_ttv.yaml'))
array_ds = TTVArrayLikeDataSource(dummy_data_source, ttv)
self.assertEqual(len(array_ds), 3)
all_values = np.fromiter((x for x in array_ds[:]), dtype='int16')
self.assertTrue(
np.all(
np.in1d(
all_values,
np.array([1, 2, 3])
)
)
)
def get_data(self, dataset, event_list=None):
# Load Basics for this dataset and shift it by 1
data = hax.minitrees.load_single_minitree(dataset, 'Basics')
df = data.shift(1)
# Add previous_ prefix to all columns
df = df.rename(columns=lambda x: 'previous_' + x)
# Add (unshifted) event number and run number, to support merging
df['event_number'] = data['event_number']
df['run_number'] = data['run_number']
# Support for event list (lame)
if event_list is not None:
df = df[np.in1d(df['event_number'].values, event_list)]
return df
def particle_mask(self):
# Dynamically create the masking array for particles, and get
# the data using standard yt methods.
if self._particle_mask is not None:
return self._particle_mask
# This is from disk.
pid = self.__getitem__('particle_index')
# This is from the sphere.
if self._name == "RockstarHalo":
ds = self.ds.sphere(self.CoM, self._radjust * self.max_radius)
elif self._name == "LoadedHalo":
ds = self.ds.sphere(self.CoM, np.maximum(self._radjust * \
self.ds.quan(self.max_radius, 'code_length'), \
self.ds.index.get_smallest_dx()))
sp_pid = ds['particle_index']
self._ds_sort = sp_pid.argsort()
sp_pid = sp_pid[self._ds_sort]
# This matches them up.
self._particle_mask = np.in1d(sp_pid, pid)
return self._particle_mask
def extract_from_volume(vol_data, vox_ijk):
"""Extract data values (broadcasting across time if relevant)."""
i, j, k = vox_ijk.T
ii, jj, kk = vol_data.shape[:3]
fov = (np.in1d(i, np.arange(ii)) &
np.in1d(j, np.arange(jj)) &
np.in1d(k, np.arange(kk)))
if len(vol_data.shape) == 3:
ntp = 1
else:
ntp = vol_data.shape[-1]
roi_data = np.empty((len(i), ntp))
roi_data[:] = np.nan
roi_data[fov] = vol_data[i[fov], j[fov], k[fov]]
return roi_data
def clip_catalog(self):
# ROI-specific catalog
logger.debug("Clipping full catalog...")
cut_observable = self.mask.restrictCatalogToObservableSpace(self.catalog_full)
# All objects within disk ROI
logger.debug("Creating roi catalog...")
self.catalog_roi = self.catalog_full.applyCut(cut_observable)
self.catalog_roi.project(self.roi.projector)
self.catalog_roi.spatialBin(self.roi)
# All objects interior to the background annulus
logger.debug("Creating interior catalog...")
cut_interior = numpy.in1d(ang2pix(self.config['coords']['nside_pixel'], self.catalog_roi.lon, self.catalog_roi.lat),
self.roi.pixels_interior)
#cut_interior = self.roi.inInterior(self.catalog_roi.lon,self.catalog_roi.lat)
self.catalog_interior = self.catalog_roi.applyCut(cut_interior)
self.catalog_interior.project(self.roi.projector)
self.catalog_interior.spatialBin(self.roi)
# Set the default catalog
#logger.info("Using interior ROI for likelihood calculation")
self.catalog = self.catalog_interior
#self.pixel_roi_cut = self.roi.pixel_interior_cut
def inFootprint(self, pixels, nside=None):
"""
Open each valid filename for the set of pixels and determine the set
of subpixels with valid data.
"""
if numpy.isscalar(pixels): pixels = numpy.array([pixels])
if nside is None: nside = self.nside_likelihood
inside = numpy.zeros( len(pixels), dtype='bool')
if not self.nside_catalog:
catalog_pix = [0]
else:
catalog_pix = superpixel(pixels,nside,self.nside_catalog)
catalog_pix = numpy.intersect1d(catalog_pix,self.catalog_pixels)
for filenames in self.filenames[catalog_pix]:
#logger.debug("Loading %s"%filenames['mask_1'])
subpix_1,val_1 = ugali.utils.skymap.readSparseHealpixMap(filenames['mask_1'],'MAGLIM',construct_map=False)
#logger.debug("Loading %s"%filenames['mask_2'])
subpix_2,val_2 = ugali.utils.skymap.readSparseHealpixMap(filenames['mask_2'],'MAGLIM',construct_map=False)
subpix = numpy.intersect1d(subpix_1,subpix_2)
superpix = numpy.unique(ugali.utils.skymap.superpixel(subpix,self.nside_pixel,nside))
inside |= numpy.in1d(pixels, superpix)
return inside
def index_pixels(lon,lat,pixels,nside):
"""
Find the index for object amoung a subset of healpix pixels.
Set index of objects outside the pixel subset to -1
# ADW: Not really safe to set index = -1 (accesses last entry);
# -np.inf would be better, but breaks other code...
"""
pix = ang2pix(nside,lon,lat)
# pixels should be pre-sorted, otherwise...???
index = np.searchsorted(pixels,pix)
if np.isscalar(index):
if not np.in1d(pix,pixels).any(): index = -1
else:
# Find objects that are outside the roi
#index[np.take(pixels,index,mode='clip')!=pix] = -1
index[~np.in1d(pix,pixels)] = -1
return index
############################################################
def get(self, names=None, burn=None, clip=None):
if names is None: names = list(self.dtype.names)
names = np.array(names,ndmin=1)
missing = names[~np.in1d(names,self.dtype.names)]
if len(missing):
msg = "field(s) named %s not found"%(missing)
raise ValueError(msg)
#idx = np.where(np.in1d(self.dtype.names,names))[0]
idx = np.array([self.dtype.names.index(n) for n in names])
# Remove zero entries
zsel = ~np.all(self.ndarray==0,axis=1)
# Remove burn entries
bsel = np.zeros(len(self),dtype=bool)
bsel[slice(burn,None)] = 1
data = self.ndarray[:,idx][bsel&zsel]
if clip is not None:
from astropy.stats import sigma_clip
mask = sigma_clip(data,sig=clip,copy=False,axis=0).mask
data = data[np.where(~mask.any(axis=1))]
return data
def _setup_subpix(self,nside=2**16):
"""
Subpixels for random position generation.
"""
# Only setup once...
if hasattr(self,'subpix'): return
# Simulate over full ROI
self.roi_radius = self.config['coords']['roi_radius']
# Setup background spatial stuff
logger.info("Setup subpixels...")
self.nside_pixel = self.config['coords']['nside_pixel']
self.nside_subpixel = self.nside_pixel * 2**4 # Could be config parameter
epsilon = np.degrees(healpy.max_pixrad(self.nside_pixel)) # Pad roi radius to cover edge healpix
subpix = ugali.utils.healpix.query_disc(self.nside_subpixel,self.roi.vec,self.roi_radius+epsilon)
superpix = ugali.utils.healpix.superpixel(subpix,self.nside_subpixel,self.nside_pixel)
self.subpix = subpix[np.in1d(superpix,self.roi.pixels)]
