def set_proj_plane_info(self,xsize,ysize,lonra,latra):
if lonra is None: lonra = [-180.,180.]
if latra is None: latra = [-90.,90.]
if (len(lonra)!=2 or len(latra)!=2 or lonra[0]<-180. or lonra[1]>180.
or latra[0]<-90 or latra[1]>90 or lonra[0]>=lonra[1] or latra[0]>=latra[1]):
raise TypeError("Wrong argument lonra or latra. Must be lonra=[a,b],latra=[c,d] "
"with a<b, c<d, a>=-180, b<=180, c>=-90, d<=+90")
lonra = self._flip*np.float64(lonra)[::self._flip]
latra = np.float64(latra)
xsize = np.long(xsize)
if ysize is None:
ratio = (latra[1]-latra[0])/(lonra[1]-lonra[0])
ysize = np.long(round(ratio*xsize))
else:
ysize = np.long(ysize)
ratio = float(ysize)/float(xsize)
if max(xsize,ysize) > 2000:
if max(xsize,ysize) == xsize:
xsize = 2000
ysize = np.long(round(ratio*xsize))
else:
ysize = 2000
xsize = np.long(round(ysize/ratio))
super(CartesianProj,self).set_proj_plane_info(xsize=xsize, lonra=lonra, latra=latra,
ysize=ysize, ratio=ratio)
def set_proj_plane_info(self, xsize, ysize, lonra, latra):
if lonra is None:
lonra = [-180., 180.]
else:
# shift lonra[1] into the range [lonra[0], lonra[0]+360]
lonra_span = np.mod(lonra[1] - lonra[0], 360)
if lonra_span == 0:
lonra_span = 360
lonra[1] = lonra[0] + lonra_span
if latra is None:
latra = [-90., 90.]
if (
len(lonra) != 2
or len(latra) != 2
or latra[0] < -90
or latra[1] > 90
or latra[0] >= latra[1]
):
raise TypeError(
"Wrong argument lonra or latra. Must be lonra=[a,b],latra=[c,d] "
"c<d, c>=-90, d<=+90"
)
lonra = self._flip * np.float64(lonra)[:: self._flip]
latra = np.float64(latra)
xsize = np.long(xsize)
if ysize is None:
ratio = (latra[1] - latra[0]) / (lonra[1] - lonra[0])
ysize = np.long(round(ratio * xsize))
else:
ysize = np.long(ysize)
ratio = float(ysize) / float(xsize)
super(CartesianProj, self).set_proj_plane_info(
xsize=xsize, lonra=lonra, latra=latra, ysize=ysize, ratio=ratio
)
def ExpandDims(inputs, axis=-1, **kwargs):
"""ExpandDims interface of NDArray.
Parameters
----------
inputs : Tensor
The input tensor.
axis : int
The insert position of new dimension. Default is ``-1`` (Push Back).
Returns
-------
Tensor
The output tensor.
Examples
--------
>>> a = Tensor(shape=[1, 2, 3, 4]).Variable()
>>> print ExpandDims(a).shape
>>> print ExpandDims(a, axis=2).shape
"""
CheckInputs(inputs, 1)
arguments = ParseArguments(locals())
output = Tensor.CreateOperator(nout=1, op_type='ExpandDims', **arguments)
if inputs.shape is not None:
output.shape = inputs.shape[:]
if axis == -1 or axis >= len(inputs.shape):
output.shape.append(np.long(1))
else: output.shape.insert(axis, np.long(1))
return output
def test_intp(self,level=rlevel):
"""Ticket #99"""
i_width = np.int_(0).nbytes*2 - 1
long('0x' + 'f'*i_width,16)
#self.failUnlessRaises(OverflowError,np.intp,'0x' + 'f'*(i_width+1),16)
#self.failUnlessRaises(ValueError,np.intp,'0x1',32)
assert_equal(255,np.long('0xFF',16))
assert_equal(1024,np.long(1024))
def _create_objects(self, diaobject_data):
"""
Create a dict of diaObjects formatted according to the
appropriate avro schema
Parameters
----------
diaobject_data is a numpy recarray containing all of the
data needed for the diaObject
Returns
-------
A dict keyed on uniqueId (the CatSim unique identifier for each
astrophysical source). Each value is a properly formatted
diaObject corresponding to its key.
"""
diaobject_dict = {}
for i_object in range(len(diaobject_data)):
diaobject = diaobject_data[i_object]
avro_diaobject = {}
avro_diaobject['flags'] = np.long(self._rng.randint(10, 1000))
avro_diaobject['diaObjectId'] = np.long(diaobject['uniqueId'])
avro_diaobject['ra'] = diaobject['ra']
avro_diaobject['decl'] = diaobject['dec']
ra_dec_cov = {}
ra_dec_cov['raSigma'] = self._rng.random_sample()*0.001
ra_dec_cov['declSigma'] = self._rng.random_sample()*0.001
ra_dec_cov['ra_decl_Cov'] = self._rng.random_sample()*0.001
avro_diaobject['ra_decl_Cov'] = ra_dec_cov
avro_diaobject['radecTai'] = diaobject['TAI']
avro_diaobject['pmRa'] = diaobject['pmRA']
avro_diaobject['pmDecl'] = diaobject['pmDec']
avro_diaobject['parallax'] = diaobject['parallax']
pm_parallax_cov = {}
for field in ('pmRaSigma', 'pmDeclSigma', 'parallaxSigma', 'pmRa_pmDecl_Cov',
'pmRa_parallax_Cov', 'pmDecl_parallax_Cov'):
pm_parallax_cov[field] = 0.0
avro_diaobject['pm_parallax_Cov'] = pm_parallax_cov
avro_diaobject['pmParallaxLnL'] = self._rng.random_sample()
avro_diaobject['pmParallaxChi2'] = self._rng.random_sample()
avro_diaobject['pmParallaxNdata'] = 0
diaobject_dict[diaobject['uniqueId']] = avro_diaobject
return diaobject_dict
def run(self):
# Run until turned off
while 1:
if self.on():
# Read bytes in chunks of meaningful size
if self.ser.inWaiting() > 3:
bytes = bytearray(3)
self.ser.readinto(bytes)
height = (bytes[0] << 16) + (bytes[1] << 8) + bytes[2]
# convert to signed long
if (height >= 0x800000): # = 2^23
height = height - 0x1000000 # = 2^24
height = np.long(height)
sampleLock.acquire()
samples[self.pos, self.channel] = height
sampleLock.release()
# Update array indices
self.channel += 1
if self.channel == channels:
self.channel = 0
self.pos += 1
if self.pos == BUF_LEN:
self.pos = 0
def detectionOutput_fprop(self, conf_view, loc_view, detection, prior_boxes,
proposals, nms_top_k, image_top_k, score_threshold, nms_threshold):
conf = c_longlong(conf_view._tensor.ctypes.data)
loc = c_longlong(loc_view._tensor.ctypes.data)
detection = c_longlong(detection._tensor.ctypes.data)
prior_boxes = c_longlong(prior_boxes._tensor.ctypes.data)
L, num_class, bs = conf_view.shape
proposals = c_longlong(proposals._tensor.ctypes.data)
result = np.zeros((bs, image_top_k, 6), dtype=np.float32)
result_ptr = c_longlong(result.ctypes.data)
result_len = np.zeros(bs, dtype=np.int64)
result_len_ptr = c_longlong(result_len.ctypes.data)
self.mklEngine.detection_fprop(conf, loc, result_ptr, prior_boxes,
result_len_ptr, c_longlong(L), c_longlong(num_class),
c_longlong(bs), c_longlong(nms_top_k),
c_longlong(image_top_k),
c_float(score_threshold),
c_float(nms_threshold))
batch_all_detections = [None] * self.bsz
for i in range(bs):
leng = np.long(result_len[i])
res_batch = np.zeros((leng, 6))
res_batch[:] = result[i, 0:leng, :]
batch_all_detections[i] = res_batch
return batch_all_detections
def produce_regions(masks, visualize=False):
"""given the proposal segmentation masks for an image as a [width, height, proposal_num]
matrix outputs all regions in the image"""
width, height, n_prop = masks.shape
t = ('u8,'*int(np.math.ceil(float(n_prop) / 64)))[:-1]
bv = np.zeros((width, height), dtype=np.dtype(t))
for i in range(n_prop):
m = masks[:, :, i]
a = 'f%d' % (i / 64)
h = m * np.long(2 ** (i % 64))
if n_prop >= 64:
bv[a] += h
else:
bv += h
un = np.unique(bv)
regions = np.zeros((width, height), dtype="uint16")
for i, e in enumerate(un):
regions[bv == e] = i
if visualize:
plt.figure()
plt.imshow(regions)
plt.set_cmap('prism')
plt.colorbar()
return regions
def _get_window_sub(self, window='None'):
"""Returns the window time series and amplitude normalization term
:param window: window string
:return: w, amplitude_norm
"""
window = window.split(':')
if window[0] in ['Hamming', 'Hann']:
w = np.hanning(self.samples)
elif window[0] == 'Force':
w = np.zeros(self.samples)
force_window = float(window[1])
to1 = np.long(force_window * self.samples)
w[:to1] = 1.
elif window[0] == 'Exponential':
w = np.arange(self.samples)
exponential_window = float(window[1])
w = np.exp(np.log(exponential_window) * w / (self.samples - 1))
else: # window = 'None'
w = np.ones(self.samples)
if window[0] == 'Force':
amplitude_norm = 2 / len(w)
else:
amplitude_norm = 2 / np.sum(w)
return w, amplitude_norm
def order_paths_by_preference(sorts_list,id_list,paths_list,file_type_list,data_node_list,check_dimensions,
semaphores=dict(),time_var='time',session=None,remote_netcdf_kwargs=dict()):
#FIND ORDERING:
paths_desc = []
for id in sorts_list:
paths_desc.append((id,np.int64))
for id in id_list:
paths_desc.append((id,'a255'))
paths_ordering = np.empty((len(paths_list),), dtype=paths_desc)
if check_dimensions:
dimension_type_list = ['unqueryable',]
for file_id, file in enumerate(paths_list):
paths_ordering['path'][file_id] = file['path'].split('|')[0]
#Convert path name to 'unique' integer using hash.
#The integer will not really be unique but collisions
#should be extremely rare for similar strings with only small variations.
paths_ordering['path_id'][file_id] = hash(
paths_ordering['path'][file_id]
)
for unique_file_id in unique_file_id_list:
paths_ordering[unique_file_id][file_id] = file['path'].split('|')[unique_file_id_list.index(unique_file_id)+1]
paths_ordering['version'][file_id] = np.long(file['version'][1:])
paths_ordering['file_type'][file_id] = file['file_type']
paths_ordering['data_node'][file_id] = remote_netcdf.get_data_node(file['path'],paths_ordering['file_type'][file_id])
if check_dimensions:
#Dimensions types. Find the different dimensions types:
if not paths_ordering['file_type'][file_id] in queryable_file_types:
paths_ordering['dimension_type_id'][file_id] = dimension_type_list.index('unqueryable')
else:
remote_data = remote_netcdf.remote_netCDF(paths_ordering['path'][file_id],
paths_ordering['file_type'][file_id],
semaphores=semaphores,
session=session,
**remote_netcdf_kwargs)
dimension_type = remote_data.safe_handling(netcdf_utils.find_dimension_type,time_var=time_var)
if not dimension_type in dimension_type_list: dimension_type_list.append(dimension_type)
paths_ordering['dimension_type_id'][file_id] = dimension_type_list.index(dimension_type)
if check_dimensions:
#Sort by increasing number. Later when we sort, we should get a uniform type:
dimension_type_list_number = [ sum(paths_ordering['dimension_type_id']==dimension_type_id)
for dimension_type_id,dimension_type in enumerate(dimension_type_list)]
sort_by_number = np.argsort(dimension_type_list_number)[::-1]
paths_ordering['dimension_type_id'] = sort_by_number[paths_ordering['dimension_type_id']]
#Sort paths from most desired to least desired:
#First order desiredness for least to most:
data_node_order = copy.copy(data_node_list)[::-1]#list(np.unique(paths_ordering['data_node']))
file_type_order = copy.copy(file_type_list)[::-1]#list(np.unique(paths_ordering['file_type']))
for file_id, file in enumerate(paths_list):
paths_ordering['data_node_id'][file_id] = data_node_order.index(paths_ordering['data_node'][file_id])
paths_ordering['file_type_id'][file_id] = file_type_order.index(paths_ordering['file_type'][file_id])
#'version' is implicitly from least to most
#sort and reverse order to get from most to least:
return np.sort(paths_ordering,order = sorts_list)[::-1]
def run(self):
self.pos = 0
# This t is a global variable shared with display
while 1:
if self.on():
dataLock.acquire()
packages = len(data)
dataLock.release()
if packages > channels:
for i in range(channels):
# Don't read and write data simultaneously; acquire lock
dataLock.acquire()
bytes = data.popleft()
dataLock.release()
# construct y value
height = (bytes[0] << 16) + (bytes[1] << 8) + bytes[2]
# convert to signed long
if (height >= 0x800000): # = 2^23
height = height - 0x1000000 # = 2^24
height = np.long(height)
sampleLock.acquire()
samples[self.pos,i] = height
sampleLock.release()
self.pos += 1
if (self.pos == BUF_LEN):
self.pos = 0
def run(self):
self.pos = 0
samples = np.ctypeslib.as_array(self.raw_samples.get_obj())
samples = samples.reshape(self.BUF_LEN, self.channels)
# This t is a global variable shared with display
while self.on:
if not self.cmds.empty():
cmd = self.cmds.get()
if cmd == '+':
self.ready()
elif cmd == '-':
self.reset()
elif cmd == "Exit!":
self.on = False
else:
print cmd
if not self.paused:
for i in range(self.channels):
bytes = self.data.recv()
# construct y value
height = (bytes[0] << 16) + (bytes[1] << 8) + bytes[2]
# convert to signed long
if (height >= 0x800000): # = 2^23
height = height - 0x1000000 # = 2^24
height = np.long(height)
samples[self.pos, i] = height
self.pos += 1
if (self.pos == self.BUF_LEN):
self.pos = 0
def Stack(inputs, axis=0, **kwargs):
"""Stack the inputs along the given axis.
All dimensions of inputs should be same.
The ``axis`` can be negative.
Parameters
----------
inputs : list of Tensor
The inputs.
axis : int
The axis to stack.
Returns
-------
Tensor
The output tensor.
"""
CheckInputs(inputs, 1, INT_MAX)
arguments = ParseArguments(locals())
arguments['num_input'] = len(inputs)
output = Tensor.CreateOperator(nout=1, op_type='Stack', **arguments)
if all(input.shape is not None for input in inputs):
while axis < 0: axis += (len(inputs[0].shape) + 1)
output.shape = inputs[0].shape
output.shape.insert(axis, np.long(len(inputs)))
return output
def xml2field(self, elem, name=None):
typElem = elem.find('datatype')
dType = typElem.text
dDim = typElem.attrib['length']
dDim = np.asarray([np.long(d) for d in dDim.split()])[::-1]
dLen = np.prod(dDim)
if name is None:
name = elem.attrib['name']
valElem = elem.find('value')
if dType == 'pointer':
self.xml2field(valElem.find('parameter'), elem.attrib['name'])
return
if dType == 'struct':
o = Xml2Py(None, valElem[0])
setattr(self, name, o)
return
val = elem.find('value').text
if dLen > 1:
val = val.strip('[]').split(',')
conv = {'int': np.int, 'long': np.long, 'float': np.float, 'double': np.double, 'string': lambda s: s}
try:
if (dLen > 1):
val = np.asarray([conv[dType](v) for v in val]).reshape(dDim)
else:
val = conv[dType](val)
except KeyError:
print('WARNING: Unsupported data type {} in field {}! Ignoring...'.format(dType, name))
return
setattr(self, name, val)
def order_paths_by_preference(self):
#FIND ORDERING:
paths_desc=[]
for id in self.sorts_list:
paths_desc.append((id,np.int32))
for id in self.id_list:
paths_desc.append((id,'a255'))
paths_ordering=np.empty((len(self.paths_list),), dtype=paths_desc)
for file_id, file in enumerate(self.paths_list):
paths_ordering['path'][file_id]=file['path'].split('|')[0]
#Convert path name to 'unique' integer using hash.
#The integer will not really be unique but collisions
#should be extremely rare for similar strings with only small variations.
paths_ordering['path_id'][file_id]=hash(
paths_ordering['path'][file_id]
)
paths_ordering['checksum'][file_id]=file['path'].split('|')[1]
paths_ordering['version'][file_id]=np.long(file['version'][1:])
paths_ordering['file_type'][file_id]=file['file_type']
paths_ordering['data_node'][file_id]=retrieval_utils.get_data_node(file['path'],paths_ordering['file_type'][file_id])
#Sort paths from most desired to least desired:
#First order desiredness for least to most:
data_node_order=copy.copy(self.data_node_list)[::-1]#list(np.unique(paths_ordering['data_node']))
file_type_order=copy.copy(self.file_type_list)[::-1]#list(np.unique(paths_ordering['file_type']))
for file_id, file in enumerate(self.paths_list):
paths_ordering['data_node_id'][file_id]=data_node_order.index(paths_ordering['data_node'][file_id])
paths_ordering['file_type_id'][file_id]=file_type_order.index(paths_ordering['file_type'][file_id])
#'version' is implicitly from least to most
#sort and reverse order to get from most to least:
return np.sort(paths_ordering,order=self.sorts_list)[::-1]
def OneHot(inputs, depth, on_value=1, off_value=0, **kwargs):
"""Generate the one-hot representation of inputs.
Parameters
----------
inputs : Tensor
The input tensor.
depth : int
The depth of one-hot representation.
on_value : int
The value when ``indices[j] = i``.
off_value : int
The value when ``indices[j] != i``.
Returns
-------
Tensor
The output tensor.
"""
CheckInputs(inputs, 1)
arguments = ParseArguments(locals())
output = Tensor.CreateOperator(nout=1, op_type='OneHot', **arguments)
if inputs.shape is not None:
output.shape = inputs.shape[:]
output.shape.append(np.long(depth))
return output
def start_jobs():
"""
Restores the plots if requested and if the persistent files exist and
starts the qt timer of the 1st plot.
"""
for plot in _plots:
if plot.persistentName:
plot.restore_plots()
plot.fig.canvas.set_window_title(plot.title)
runCardVals.iteration = np.long(0)
noTimer = len(_plots) == 0 or\
(plt.get_backend().lower() in (x.lower() for x in
mpl.rcsetup.non_interactive_bk))
if noTimer:
print("The job is running... ")
while True:
msg = '{0} of {1}'.format(
runCardVals.iteration+1, runCardVals.repeats)
if os.name == 'posix':
sys.stdout.write("\r\x1b[K " + msg)
else:
sys.stdout.write("\r ")
print(msg+' ')
sys.stdout.flush()
res = dispatch_jobs()
if res:
return
else:
plot = _plots[0]
plot.areProcessAlreadyRunning = False
plot.timer = plot.fig.canvas.new_timer()
plot.timer.add_callback(plot.timer_callback)
plot.timer.start()
def ref_mjd(fits_file, hdu=1):
"""Read MJDREFF+ MJDREFI or, if failed, MJDREF, from the FITS header.
Parameters
----------
fits_file : str
Returns
-------
mjdref : numpy.longdouble
the reference MJD
Other Parameters
----------------
hdu : int
"""
import collections
if isinstance(fits_file, collections.Iterable) and\
not is_string(fits_file): # pragma: no cover
fits_file = fits_file[0]
logging.info("opening %s" % fits_file)
try:
ref_mjd_int = np.long(read_header_key(fits_file, 'MJDREFI'))
ref_mjd_float = np.longdouble(read_header_key(fits_file, 'MJDREFF'))
ref_mjd_val = ref_mjd_int + ref_mjd_float
except: # pragma: no cover
ref_mjd_val = np.longdouble(read_header_key(fits_file, 'MJDREF'))
return ref_mjd_val
def dimshuffle(self, *args, **kwargs):
"""Shuffle the dimensions. [**Theano Style**]
Parameters
----------
dimensions : list
The desired dimensions.
Returns
-------
Tensor
The dimshuffled output.
"""
dimensions = list(args)
perms = []
for dim in dimensions:
if dim != 'x':
if not isinstance(dim, int):
raise ValueError('The type of dimension should be int.')
perms.append(dim)
# transpose
output = Tensor.CreateOperator(inputs=self, nout=1,
op_type='Transpose', perms=perms, **kwargs)
if self.shape is not None:
if len(self.shape) != len(perms):
raise ValueError('The ndim of inputs is {}, but perms provide {}'. \
format(len(self.shape), len(perms)))
output.shape = self.shape[:]
for i, axis in enumerate(perms):
output.shape[i] = self.shape[axis]
# expand dims
for i in xrange(len(dimensions) - len(perms)):
flag = False
input_shape = output.shape
axis = -1
for idx in xrange(len(dimensions)):
if idx >= len(perms): continue
cur_dim = perms[idx]; exp_dim = dimensions[idx]
if cur_dim != exp_dim:
axis = idx
output = Tensor.CreateOperator(inputs=output, nout=1,
op_type='ExpandDims', axis=axis)
perms.insert(axis, 'x')
flag = True
break
if not flag:
axis = len(perms)
output = Tensor.CreateOperator(inputs=output, nout=1,
op_type='ExpandDims', axis=len(perms))
perms.append('x')
if self.shape is not None:
output.shape = input_shape[:]
output.shape.insert(axis, np.long(1))
return output
def const_rebin(x, y, factor, yerr=None, normalize=True):
"""Rebin any pair of variables.
Might be time and counts, or freq and pds.
Also possible to rebin the error on y.
Parameters
----------
x : array-like
y : array-like
factor : int
Rebin factor
yerr : array-like, optional
Uncertainties of y values (it is assumed that the y are normally
distributed)
Returns
-------
new_x : array-like
The rebinned x array
new_y : array-like
The rebinned y array
new_err : array-like
The rebinned yerr array
Other Parameters
----------------
normalize : bool
"""
arr_dtype = y.dtype
if factor <= 1:
res = [x, y]
if yerr is not None:
res.append(yerr)
else:
res.append(np.zeros(len(y), dtype=arr_dtype))
return res
factor = np.long(factor)
nbin = len(y)
new_nbins = np.int(nbin / factor)
y_resh = np.reshape(y[:new_nbins * factor], (new_nbins, factor))
x_resh = np.reshape(x[:new_nbins * factor], (new_nbins, factor))
new_y = np.sum(y_resh, axis=1)
new_x = np.sum(x_resh, axis=1) / factor
if yerr is not None:
yerr_resh = np.reshape(yerr[:new_nbins * factor], (new_nbins, factor))
new_yerr = np.sum(yerr_resh ** 2, axis=1)
else:
new_yerr = np.zeros(len(new_x), dtype=arr_dtype)
if normalize:
return new_x, new_y / factor, np.sqrt(new_yerr) / factor
else:
return new_x, new_y, np.sqrt(new_yerr)
def run(data, p, m, n, b, c):
"""
Starts the main LSH process.
Parameters
----------
zdata : RDD[Vector]
RDD of data points. Acceptable vector types are numpy.ndarray
or PySpark SparseVector.
p : integer, larger than the largest value in data.
m : integer, number of bins for hashing.
n : integer, number of rows to split the signatures into.
b : integer, number of bands.
c : integer, minimum allowable cluster size.
"""
#data.zipWithIndex()
zdata = data
seeds = np.vstack([np.random.random_integers(p, size = n), np.random.random_integers(0, p, size = n)]).T
hashes = [functools.partial(minhash, a = s[0], b = s[1], p = p, m = m) for s in seeds]
# Start by generating the signatures for each data point.
# Output format is:
# <(vector idx, band idx), minhash>
sigs = zdata.flatMap(lambda x: [[(x[1], i % b), hashes[i](x[0])] for i, h in enumerate(hashes)]).cache()
# Put together the vector minhashes in the same band.
# Output format is:
# <(band idx, minhash list), vector idx>
bands = sigs.groupByKey() \
.map(lambda x: [(x[0][1], hash(frozenset(x[1].data))), x[0][0]]) \
.groupByKey().cache()
# Should we filter?
if c > 0:
bands = bands.filter(lambda x: len(x[1]) > c).cache()
# Remaps each element to a cluster / bucket index.
# Output format is:
# <vector idx, bucket idx>
vector_bucket = bands.map(lambda x: frozenset(sorted(x[1]))).distinct() \
.zipWithIndex().flatMap(lambda x: map(lambda y: (np.long(y), x[1]), x[0])) \
.cache()
# Reverses indices, to key the vectors by their buckets.
# Output format is:
# <bucket idx, vector idx>
bucket_vector = vector_bucket.map(lambda x: (x[1], x[0])).cache()
# Joins indices up with original data to provide clustering results.
# Output format is:
# <bucket idx, list of vectors>
buckets = zdata.map(lambda x: (x[1], x[0])).join(vector_bucket) \
.map(lambda x: (x[1][1], x[1][0])).groupByKey().cache()
# Computes Jaccard similarity of each bucket.
scores = buckets.map(distance_metric).cache()
# Return a wrapper object around the metrics of interest.
return PyLSHModel(sigs, bands, vector_bucket, bucket_vector, buckets, scores)
def get_coincidences(fp, st_start_ch0, st_start_ch1, st_len, pulse_sep):
pqf = h5py.File(fp, 'r')
sp = pqf['/PQ_special-1'].value
ch = pqf['/PQ_channel-1'].value
sn = pqf['/PQ_sync_number-1'].value
st = pqf['/PQ_sync_time-1'].value
tt = pqf['/PQ_time-1'].value
pqf.close()
fltr_w1_ch0 = (((st_start_ch0 <= st) & (st < (st_start_ch0 + st_len))) & (ch == 0) & (sp == 0))
fltr_w1_ch1 = (((st_start_ch1 <= st) & (st < (st_start_ch1 + st_len))) & (ch == 1) & (sp == 0))
fltr_w2_ch0 = (((st_start_ch0 + pulse_sep <= st) & (st < (st_start_ch0 + pulse_sep + st_len))) & (ch == 0) & (sp == 0))
fltr_w2_ch1 = (((st_start_ch1 + pulse_sep <= st) & (st < (st_start_ch1 + pulse_sep + st_len))) & (ch == 1) & (sp == 0))
fltr0 = fltr_w1_ch0 | fltr_w2_ch0
fltr1 = fltr_w1_ch1 | fltr_w2_ch1
st0 = st[fltr0]
t0 = tt[fltr0]
sn0 = sn[fltr0]
st1 = st[fltr1]
t1 = tt[fltr1]
sn1 = sn[fltr1]
samesync0 = np.in1d(sn0, sn1)
samesync1 = np.in1d(sn1, sn0)
c_st0 = st0[samesync0]
c_st1 = st1[samesync1]
c_t0 = t0[samesync0]
c_sn0 = sn0[samesync0]
c_t1 = t1[samesync1]
c_sn1 = sn1[samesync1]
coincidences = np.empty((0,4), dtype = np.int64)
for _sn0, _t0, _st0 in zip(c_sn0, c_t0, c_st0):
_c = c_sn1==_sn0
for _t1, _st1 in zip(c_t1[_c], c_st1[_c]):
dt = np.long(_t0) - np.long(_t1)
coincidences = np.vstack((coincidences, np.array([dt, _st0, _st1, _sn0], dtype = _tpqi_dtype)))
return coincidences
def get_ts(self, idx):
"""
Get a time series from the binary file.
Parameters
----------
idx : tuple of ints, or a list of a tuple of ints
idx can be (layer, row, column) or it can be a list in the form
[(layer, row, column), (layer, row, column), ...]. The layer,
row, and column values must be zero based.
Returns
----------
out : numpy array
Array has size (ntimes, ncells + 1). The first column in the
data array will contain time (totim).
See Also
--------
Notes
-----
The layer, row, and column values must be zero-based, and must be
within the following ranges: 0 <= k < nlay; 0 <= i < nrow; 0 <= j < ncol
Examples
--------
"""
kijlist = self._build_kijlist(idx)
nstation = self._get_nstation(idx, kijlist)
# Initialize result array and put times in first column
result = self._init_result(nstation)
istat = 1
for k, i, j in kijlist:
recordlist = []
ioffset = (i * self.ncol + j) * self.realtype(1).nbytes
for irec, header in enumerate(self.recordarray):
ilay = header['ilay'] - 1 # change ilay from header to zero-based
if ilay != k:
continue
ipos = self.iposarray[irec]
# Calculate offset necessary to reach intended cell
self.file.seek(ipos + np.long(ioffset), 0)
# Find the time index and then put value into result in the
# correct location.
itim = np.where(result[:, 0] == header['totim'])[0]
result[itim, istat] = binaryread(self.file, self.realtype)
istat += 1
return result
def predict_entry(self, entry):
inner = torch.ones(self.rank)
for dim, col in enumerate(entry):
col = Variable(torch.LongTensor([np.long(col)]))
inner *= self.factors[dim](col)[0]
if self.datatype == "real":
return float(torch.sum(inner))
elif self.datatype == "binary":
return 1 if torch.sum(inner) > 0 else 0
elif self.datatype == "count":
return float(torch.sum(inner))
def run(self):
self.pos = 0
self.channel = 0
samples = np.ctypeslib.as_array(self.raw_samples.get_obj())
samples = samples.reshape(self.BUF_LEN, self.channels)
self.ser = serial.Serial(6, baudrate=57600, timeout=1)
self.ser.flushInput()
self.reset()
self.ready()
ctrl_bytes = bytearray(3)
bytes = bytearray(3 * self.channels)
# Run until turned off
while self.on:
# Read and execute control commands from main process
if not self.cmds.empty():
cmd = self.cmds.get()
if cmd == '+':
self.ready()
elif cmd == '-':
self.reset()
elif cmd == "Exit!":
self.on = False
else:
print cmd
# While on, continuously empty serial port
if not self.paused:
# Read bytes in chunks of meaningful size
if self.ser.inWaiting() > 27:
self.ser.readinto(ctrl_bytes)
if (ctrl_bytes[0] == 192 and ctrl_bytes[1] == 0 and ctrl_bytes[2] == 0):
self.ser.readinto(bytes)
for channel in range(self.channels):
offset = 3 * channel
height = (bytes[offset] << 16) + (bytes[offset + 1] << 8) + bytes[offset + 2]
# convert to signed long
if (height >= 0x800000): # = 2^23
height = height - 0x1000000 # = 2^24
height = np.long(height)
samples[self.pos, channel] = height
self.pos += 1
self.sample_count.value += 1
if self.pos == self.BUF_LEN:
self.pos = 0
else:
shift = bytearray(1)
self.ser.readinto(shift)
def communicate_smart_meter(conn):
global sm_conns, NUM_TIME_INSTANCES, ppn,recv_shares_count,e,s,times
lock.acquire()
s = time.time()
string = ""
string += receive_shares(conn)
shares_time_instances = string.split(" ")
# print(shares_time_instances)
meter_id = int(shares_time_instances[0])
ppn.update_billing_dict(meter_id, shares_time_instances[1])
ppn.update_spatial_counter(shares_time_instances[1])
constant = long(ppn.get_spatial_counter()) * long(ppn.get_lagrange_multiplier())
ppn.calc_sum(constant)
# print("const", constant)
ppn.set_total_consumption(ppn.sumofshares)
recv_shares_count += 1
# time.sleep(0.015)
e = time.time()
# print( e - s)
lock.release()
def getHeader(f):
"""Extract scan information such as
"scanSize" (number of energy points in the XAS scan
"detSize" (number of detector pixels for multi-element dets.; e.g. 100)
Returns:
list of above parameters
"""
# work through header to get data dimensions (as LONGintegers)
# (do step-by-step for better code readability)
#
found = searchStrStarts(f, '# Total req')
info = found.split('=')[1]
info = info.split('x')
scanSize = np.long(info[0]) # "scanSize" = number of energy points in XAFS scan
if len(info) > 1:
detSize = np.long(info[1]) # check for 2nd dimension
else: # if not present, then detSize = 0
detSize = 0 # (i.e., transmission XAS scan only)
return scanSize, detSize
def master_wigner3j2(il1, il2, il3, lnwpro):
l1 = np.long(il1)
l2 = np.long(il2)
l3 = il3 #np.int(il3)
L = l1 + l2 + l3
L_2 = L / 2
L_2 = L_2.astype(int)
min = abs(l1 - l2)
max = l1 + l2
c = l3 * 0.
w = np.logical_and(np.logical_and((L_2 * 2 - L) == 0., l3 >= min),
l3 <= max)
good = np.where(w == True)[0]
if len(w[good]) > 0:
lnw1 = lnwpro[L_2[good] - l1]
lnw2 = lnwpro[L_2[good] - l2]
lnw3 = lnwpro[L_2[good] - l3[good]]
lnwl = lnwpro[L_2[good]]
lnc = -np.log(L[good] + 1.0) - lnwl + lnw1 + lnw2 + lnw3
c[good] = np.exp(lnc)
return c
def __init__(self,
bit,
num_filter,
kernel,
stride=[],
pad=[],
no_bias=False,
workspace=1024,
name=None):
super(IntConvProp, self).__init__(True)
# we use constant bias here to illustrate how to pass arguments
# to operators. All arguments are in string format so you need
# to convert them back to the type you want.
self.num_bit = np.long(bit)
self.num_filter = np.long(num_filter)
self.kernel = kernel
self.stride = stride
self.pad = pad
self.no_bias = no_bias
self.workspace = workspace
self.name = name
def de_weight(face_info, cache):
appid = face_info['app_id']
people_id = face_info['id']
# print(people_id, type(people_id))
# if type(people_id)
# print(people_id)
if np.long(people_id) not in cache:
cache[people_id] = appid
return True
else:
return False
def __getitem__(self, index):
'Generates one sample of data'
# Select sample
ID = self.list_IDs[index, :, :, :]
#Load data and get label
X = torch.from_numpy(ID).float()
X_data = X.permute(2, 0, 1)
y = (np.long(self.labels[index]))
return X_data, y
def bin_intervals_from_gtis(gtis, chunk_length, time):
"""Similar to intervals_from_gtis, but given an input time array.
Used to start each FFT/PDS/cospectrum from the start of a GTI,
and stop before the next gap in data (end of GTI).
In this case, it is necessary to specify the time array containing the
times of the light curve bins.
Returns start and stop bins of the intervals to use for the PDS
Parameters
----------
gtis : 2-d float array
[[gti0_0, gti0_1], [gti1_0, gti1_1], ...]
chunk_length : float
Length of the chunks
time : array-like
Times of light curve bins
Returns
-------
spectrum_start_bins : array-like
List of starting bins in the original time array to use in spectral
calculations.
spectrum_stop_bins : array-like
List of end bins to use in the spectral calculations.
"""
bintime = time[1] - time[0]
nbin = np.long(chunk_length / bintime)
spectrum_start_bins = np.array([], dtype=np.long)
for g in gtis:
if g[1] - g[0] < chunk_length:
continue
good = (time - bintime / 2 > g[0])&(time + bintime / 2 < g[1])
t_good = time[good]
if len(t_good) == 0:
continue
startbin = np.argmin(np.abs(time - bintime / 2 - g[0]))
stopbin = np.argmin(np.abs(time + bintime / 2 - g[1]))
if time[startbin] < g[0]: startbin += 1
if time[stopbin] < g[1] + bintime/2: stopbin += 1
newbins = np.arange(startbin, stopbin - nbin + 1, nbin,
dtype=np.long)
spectrum_start_bins = \
np.append(spectrum_start_bins,
newbins)
assert len(spectrum_start_bins) > 0, \
("No GTIs are equal to or longer than chunk_length.")
return spectrum_start_bins, spectrum_start_bins + nbin
def getHeader(f):
"""Extract scan information such as
"scanSize" (number of energy points in the XAS scan
"detSize" (number of detector pixels for multi-element dets.; e.g. 100)
Returns:
list of above parameters
"""
# work through header to get data dimensions (as LONGintegers)
# (do step-by-step for better code readability)
#
found = searchStrStarts(f, '# Total req')
info = found.split('=')[1]
info = info.split('x')
scanSize = np.long(
info[0]) # "scanSize" = number of energy points in XAFS scan
if len(info) > 1:
detSize = np.long(info[1]) # check for 2nd dimension
else: # if not present, then detSize = 0
detSize = 0 # (i.e., transmission XAS scan only)
return scanSize, detSize
def load_model(projection_matrix_txt, vocab_file, latent_dims=100):
v2i = {}
with codecs.open(vocab_file, 'r', 'utf-8') as vf:
for idx, line in enumerate(vf):
v2i[line.strip()] = idx
with open(projection_matrix_txt, 'r') as pf:
header_items = pf.readline().strip().split(' ')
assert len(header_items) == 2
rows, cols = np.long(header_items[0]), np.long(header_items[1])
mat = np.empty((rows, cols), dtype=np.double)
for row, line in enumerate(pf):
assert row < rows
elems = [np.double(el) for el in line.strip().split(' ')]
assert len(elems) == cols
mat[row,:] = elems
P = mat.T
return WtmfModel(P, v2i, latent_dims=latent_dims)
def to_binary(self, val):
# """
# PWM value (100% == 156)
# Bit select for PWM repetition which have value PWM+1
# """
val = val / 1.8
assert val >= 0
assert val <= 1
out = intbv(0, min=0, max=2**32)
tmp = np.long(np.round(val * (17 * 157 - 1)))
out[32:16] = tmp // 17
out[16:0] = 2**tmp % 17 - 1
return out[32:]._val
def to_binary(self, val):
# """
# PWM value (100% == 156)
# Bit select for PWM repetition which have value PWM+1
# """
val = val/1.8
assert val>=0
assert val<=1
out = intbv(0, min=0, max=2**32)
tmp = np.long(np.round(val*(17*157-1)))
out[32:16] = tmp//17
out[16:0] = 2**tmp%17-1
return out[32:]._val
def bin_intervals_from_gtis(gtis, chunk_length, time):
"""Similar to intervals_from_gtis, but given an input time array.
Used to start each FFT/PDS/cospectrum from the start of a GTI,
and stop before the next gap in data (end of GTI).
In this case, it is necessary to specify the time array containing the
times of the light curve bins.
Returns start and stop bins of the intervals to use for the PDS
Parameters
----------
gtis : 2-d float array
[[gti0_0, gti0_1], [gti1_0, gti1_1], ...]
chunk_length : float
Length of the chunks
time : array-like
Times of light curve bins
Returns
-------
spectrum_start_bins : array-like
List of starting bins in the original time array to use in spectral
calculations.
spectrum_stop_bins : array-like
List of end bins to use in the spectral calculations.
"""
bintime = time[1] - time[0]
nbin = np.long(chunk_length / bintime)
spectrum_start_bins = np.array([], dtype=np.long)
for g in gtis:
if g[1] - g[0] < chunk_length:
continue
good = (time - bintime / 2 > g[0]) & (time + bintime / 2 < g[1])
t_good = time[good]
if len(t_good) == 0:
continue
startbin = np.argmin(np.abs(time - bintime / 2 - g[0]))
stopbin = np.argmin(np.abs(time + bintime / 2 - g[1]))
if time[startbin] < g[0]: startbin += 1
if time[stopbin] < g[1] + bintime / 2: stopbin += 1
newbins = np.arange(startbin, stopbin - nbin + 1, nbin, dtype=np.long)
spectrum_start_bins = \
np.append(spectrum_start_bins,
newbins)
assert len(spectrum_start_bins) > 0, \
("No GTIs are equal to or longer than chunk_length.")
return spectrum_start_bins, spectrum_start_bins + nbin
def get_simple_landmarks(image): faces = faceCascade.detectMultiScale(image, scaleFactor=1.3, minNeighbors=4, minSize=(100, 100), flags=cv2.CASCADE_SCALE_IMAGE) if len(faces) == 0: return [] for (x,y,w,h) in faces: dlib_rect = dlib.rectangle( np.long(x),np.long(y),np.long(x+w),np.long(y+h)) detected_landmarks = predictor(image, dlib_rect).parts() #print(detected_landmarks) points = [] points = [[p.x, p.y] for p in detected_landmarks] # points to array landmarks = np.matrix(points) # Calculate NoseAngle from landmarks noseAngle = head.CalculateNoseAngle(landmarks) #print(noseAngle) # we need a gray image copy first gray_copy = cv2.cvtColor(image,cv2.COLOR_RGB2GRAY) # perform Edge Detection edgesImage = head.PerformEdgeDetection(gray_copy) topOfHeadCoords,ToH_YMin,ToH_YMax,ToH_YMaxEdge,ToH_final = head.GetTopOfHeadValues(landmarks,edgesImage) # append Toh to array points.append([ToH_final[0],ToH_final[1]]) # create matrix landmarks = np.matrix(points) # add new toh to landmark matrix #print(landmarks) return landmarks # TODOOOOOOOOOOO - return additional parameter as TOP OF HEAD AND REDO EVERYTHING !!!!!!!!!!!!!!!
def __data_generation(self, samples, fields, IDs):
'Generates data containing batch_size samples' # X : (n_samples, *dim, n_channels)
# Initialization
# Generate data
NameA = fields[IDs]
va = np.long(fields[IDs + 1])
NameB = fields[IDs + 2]
vb = np.long(fields[IDs + 3])
Name = NameA[0:2]
x = vb - va
dis = 150
win = x if x < dis else dis
diff = x - dis
start = 0 if diff <= 0 else rd.randrange(0, diff, 30)
print('diff, start: %d,%d' % (diff, start))
X = np.empty((self.samples, vb - va, *self.dim, self.n_channels))
y = np.empty((self.samples), dtype=int)
for i in range(0, win):
# load the image
fileName = self.root + samples + '/_Color_' + str(va + i +
start) + '.png'
image = cv2.imread(fileName)
# convert image to numpy array
# Store sample
gray_image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
gray_image2 = cv2.resize(gray_image, (100, 100))
data = np.expand_dims(gray_image2, axis=-1)
X[0, i, ] = data
# Store class
y[0] = self.labels[Name]
return X, tensorflow.keras.utils.to_categorical(
y, num_classes=self.n_classes)
def _callback(res):
nonlocal frame_count, last_frame, last_1_frame_cost, last_2_frame_cost, last_3_frame_cost, time_count, mach_time_factor, \
jank_count, big_jank_count, jank_time_count, _list, count_time
if type(res.plist) is InstrumentRPCParseError:
for args in kperf_data(res.raw.get_selector()):
_time, code = args[0], args[7]
if code == 830472984:
if not last_frame:
last_frame = long(_time)
else:
this_frame_cost = (long(_time) - last_frame) * mach_time_factor
if all([last_3_frame_cost != 0, last_2_frame_cost != 0, last_1_frame_cost != 0]):
if this_frame_cost > mean([last_3_frame_cost, last_2_frame_cost, last_1_frame_cost]) * 2 \
and this_frame_cost > MOVIE_FRAME_COST * NANO_SECOND * 2:
jank_count += 1
jank_time_count += this_frame_cost
if this_frame_cost > mean(
[last_3_frame_cost, last_2_frame_cost, last_1_frame_cost]) * 3 \
and this_frame_cost > MOVIE_FRAME_COST * NANO_SECOND * 3:
big_jank_count += 1
last_3_frame_cost, last_2_frame_cost, last_1_frame_cost = last_2_frame_cost, last_1_frame_cost, this_frame_cost
time_count += this_frame_cost
last_frame = long(_time)
frame_count += 1
else:
time_count = (datetime.now().timestamp() - count_time) * NANO_SECOND
if time_count > NANO_SECOND:
callback(
{"currentTime": str(datetime.now()), "FPS": frame_count / time_count * NANO_SECOND,
"jank": jank_count,
"big_jank": big_jank_count, "stutter": jank_time_count / time_count})
jank_count = 0
big_jank_count = 0
jank_time_count = 0
frame_count = 0
time_count = 0
count_time = datetime.now().timestamp()
def decrypt(encryptedBlock, key):
encoded = blockConverter(encryptedBlock[0] + encryptedBlock[1] +
encryptedBlock[2] + encryptedBlock[3])
enlength = len(encoded)
A = long(encoded[0], 2)
B = long(encoded[1], 2)
C = long(encoded[2], 2)
D = long(encoded[3], 2)
cipher = []
cipher.append(A)
cipher.append(B)
cipher.append(C)
cipher.append(D)
r = 10
w = 32
modulo = 2**32
lgw = 5
C = (C - key[2 * r + 3]) % modulo
A = (A - key[2 * r + 2]) % modulo
for j in range(1, r + 1):
i = r + 1 - j
(A, B, C, D) = (D, A, B, C)
u_temp = (D * (2 * D + 1)) % modulo
u = ROL(u_temp, lgw, 32)
t_temp = (B * (2 * B + 1)) % modulo
t = ROL(t_temp, lgw, 32)
tmod = t % 32
umod = u % 32
C = (ROR((C - key[2 * i + 1]) % modulo, tmod, 32) ^ u)
A = (ROR((A - key[2 * i]) % modulo, umod, 32) ^ t)
D = (D - key[1]) % modulo
B = (B - key[0]) % modulo
orgi = []
orgi.append(A)
orgi.append(B)
orgi.append(C)
orgi.append(D)
return cipher, orgi
def enable_auto_reply():
"""Enable auto reply.
Returns:Draft object, including reply message and response meta data.
Load pre-authorized user credentials from the environment.
TODO(developer) - See https://developers.google.com/identity
for guides on implementing OAuth2 for the application.
"""
creds, _ = google.auth.default()
try:
# create gmail api client
service = build('gmail', 'v1', credentials=creds)
epoch = datetime.utcfromtimestamp(0)
now = datetime.now()
start_time = (now - epoch).total_seconds() * 1000
end_time = (now + timedelta(days=7) - epoch).total_seconds() * 1000
vacation_settings = {
'enableAutoReply': True,
'responseBodyHtml': "I am on vacation and will reply when I am "
"back in the office. Thanks!",
'restrictToDomain': True,
'startTime': long(start_time),
'endTime': long(end_time)
}
# pylint: disable=E1101
response = service.users().settings().updateVacation(
userId='me', body=vacation_settings).execute()
print(F'Enabled AutoReply with message: '
F'{response.get("responseBodyHtml")}')
except HttpError as error:
print(F'An error occurred: {error}')
response = None
return response
def ExpandDims(inputs, axis, **kwargs):
"""Expand the new dimension with size 1 to specific axis.
Negative ``axis`` is equal to ``axis = axis + num_axes + 1``.
Parameters
----------
inputs : Tensor
The input tensor.
axis : int
The insert axis of new dimension.
Returns
-------
Tensor
The output tensor.
Examples
--------
>>> a = Tensor(shape=[1, 2, 3, 4]).Variable()
>>> print(ExpandDims(a).shape)
>>> print(ExpandDims(a, axis=2).shape)
"""
CheckInputs(inputs, 1)
arguments = ParseArguments(locals())
output = Tensor.CreateOperator(nout=1, op_type='ExpandDims', **arguments)
if inputs.shape is not None:
output.shape = inputs.shape[:]
axis += (0 if axis >= 0 else len(inputs.shape) + 1)
if axis < 0 or axis >= len(inputs.shape):
output.shape.append(np.long(1))
else:
output.shape.insert(axis, np.long(1))
return output
def arduino_dataIn(channel, data):
# read the available data
data_available = arduino_in.decode(data)
global sensors_ir, encoders, motor_status, extra_io, Data_Unpacked, sensor_distance
# update the IR sensors values
sensors_ir = np.array([data_available.extreme_left, data_available.left, data_available.center, data_available.right, data_available.extreme_right])
# update the encoders
encoders = np.array([np.long(data_available.encoder_left), np.long(data_available.encoder_right)])
# update the motor status
motor_status = data_available.motorEnable
# update the extra IOs data
extra_io = np.array([data_available.extra_io1, data_available.extra_io2])
# update the sensor distance read
temp = data_available.distance
if temp < 450:
sensor_distance = temp
# for debugging
Data_Unpacked = str(sensors_ir) + ',' + str(encoders) + ',' + str(motor_status) + ',' + str(extra_io) + ',' + str(sensor_distance)
def get_rng_states(size, seed=1):
"Return `size` number of CUDA random number generator states."
rng_states = driver.mem_alloc(np.long(size * SIZEOF_GENERATOR))
init_rng = mod.get_function('init_rng')
init_rng(np.int32(size),
rng_states,
np.uint64(seed),
np.uint64(0),
block=(BLOCK_SIZE, 1, 1),
grid=(math.ceil(float(size) / BLOCK_SIZE), 1))
return rng_states
def set_proj_plane_info(self, xsize, ysize, lonra, latra):
if lonra is None: lonra = [-180., 180.]
if latra is None: latra = [-90., 90.]
if (len(lonra) != 2 or len(latra) != 2 or lonra[0] < -180.
or lonra[1] > 180. or latra[0] < -90 or latra[1] > 90
or lonra[0] >= lonra[1] or latra[0] >= latra[1]):
raise TypeError(
"Wrong argument lonra or latra. Must be lonra=[a,b],latra=[c,d] "
"with a<b, c<d, a>=-180, b<=180, c>=-90, d<=+90")
lonra = self._flip * np.float64(lonra)[::self._flip]
latra = np.float64(latra)
xsize = np.long(xsize)
if ysize is None:
ratio = (latra[1] - latra[0]) / (lonra[1] - lonra[0])
ysize = np.long(round(ratio * xsize))
else:
ysize = np.long(ysize)
ratio = float(ysize) / float(xsize)
super(CartesianProj, self).set_proj_plane_info(xsize=xsize,
lonra=lonra,
latra=latra,
ysize=ysize,
ratio=ratio)
def expand_rpeaks(self, rpeaks):
if len(rpeaks) == 0:
return np.zeros(self.all_ws), np.zeros(self.all_ws)
normal_rpeaks = np.zeros(self.all_ws)
onehot_rpeaks = np.zeros(self.all_ws)
for rpeak in rpeaks:
nor_rpeaks = st.norm.pdf(np.arange(0, self.all_ws),
loc=rpeak,
scale=self.sigma)
normal_rpeaks = normal_rpeaks + nor_rpeaks
# onthot expands (-50 ~ +70)
st_ix = np.clip(rpeak - 50 // (1000 / self.sampling_rate), 0,
self.all_ws)
ed_ix = np.clip(rpeak + 70 // (1000 / self.sampling_rate), 0,
self.all_ws)
st_ix = np.long(st_ix)
ed_ix = np.long(ed_ix)
onehot_rpeaks[st_ix:ed_ix] = 1
# scale to [0, 1]
if self.scaled_exp:
normal_rpeaks = (normal_rpeaks - np.min(normal_rpeaks))
normal_rpeaks = normal_rpeaks / np.ptp(normal_rpeaks)
return np.array(normal_rpeaks), np.array(onehot_rpeaks)
def __getitem__(self, index):
"""Get images and target for data loader.
Args:
index (int): Index
Returns:
tuple: (image, target) where target is index of the target class.
"""
img, label = self.train_data[index, ::], self.train_labels[index]
if self.transform is not None:
img = self.transform(img)
label = np.long(label)
# label = torch.LongTensor([np.int64(label).item()])
# label = torch.FloatTensor([label.item()])
return img, label
def Arange(start, stop=None, step=1, dtype='FLOAT32', **kwargs):
"""Return a vector of elements by arange.
If ``stop`` is None, use the range: [0, start).
Parameters
----------
start : int or Tensor
The start of the range.
stop : int or Tensor
The stop of range.
step : int or Tensor
The interval between two elements.
dtype : str
The data type. ``FLOAT32`` or ``INT32``.
Returns
-------
Tensor
The vector.
"""
arguments = ParseArguments(locals())
arguments['extra_inputs'] = []
if not isinstance(start, Tensor): arguments['static_start'] = int(start)
else:
arguments['dynamic_start'] = start.name
arguments['extra_inputs'].append(start)
if stop is not None:
if not isinstance(stop, Tensor): arguments['static_stop'] = int(stop)
else:
arguments['dynamic_stop'] = stop.name
arguments['extra_inputs'].append(stop)
del arguments['stop']
if not isinstance(step, Tensor): arguments['static_step'] = int(step)
else:
arguments['dynamic_step'] = step.name
arguments['extra_inputs'].append(step)
del arguments['start']; del arguments['step']
output = Tensor.CreateOperator([], nout=1, op_type='Arange', **arguments)
if 'static_start' in arguments and \
'static_step' in arguments:
if 'dynamic_stop' not in arguments:
if stop is None: stop = start; start = 0
count = (stop - start - 1) / step + 1
output.shape = [np.long(count)]
return output
def read_keyword(self, ii):
''' --------------------------------------------------------------
Read the content of keyword of given index.
Parameters:
----------
- ii: index of the keyword to read
-------------------------------------------------------------- '''
kwsz = self.kwsz # keyword SHM data structure size
k0 = self.im_offset + self.img_len + ii * kwsz # kword offset
# ------------------------------------------
# read from SHM
# ------------------------------------------
kwlen = struct.calcsize(self.kwfmt0)
kname, ktype = struct.unpack(self.kwfmt0, self.buf[k0:k0 + kwlen])
# ------------------------------------------
# depending on type, select parsing strategy
# ------------------------------------------
kwfmt = '16s 80s'
if ktype == b'L': # keyword value is int64
kwfmt = 'q 8x 80s'
elif ktype == b'D': # keyword value is double
kwfmt = 'd 8x 80s'
elif ktype == b'S': # keyword value is string
kwfmt = '16s 80s'
elif ktype == b'N': # keyword is unused
kwfmt = '16s 80s'
kval, kcomm = struct.unpack(kwfmt, self.buf[k0 + kwlen:k0 + kwsz])
if kwfmt == '16s 80s':
kval = str(kval).strip('\x00')
# ------------------------------------------
# fill in the dictionary of keywords
# ------------------------------------------
if (ktype == b'L'):
self.kwds[ii]['value'] = np.long(kval)
elif (ktype == b'D'):
self.kwds[ii]['value'] = np.double(kval)
else:
self.kwds[ii]['value'] = ktype.decode('ascii').strip('\x00')
self.kwds[ii]['name'] = kname.decode('ascii').strip('\x00')
self.kwds[ii]['type'] = ktype.decode('ascii')
self.kwds[ii]['comment'] = kcomm.decode('ascii').strip('\x00')
def test_type_aliases(self):
# from builtins
self.assert_deprecated(lambda: np.bool(True))
self.assert_deprecated(lambda: np.int(1))
self.assert_deprecated(lambda: np.float(1))
self.assert_deprecated(lambda: np.complex(1))
self.assert_deprecated(lambda: np.object())
self.assert_deprecated(lambda: np.str('abc'))
# from np.compat
self.assert_deprecated(lambda: np.long(1))
self.assert_deprecated(lambda: np.unicode('abc'))
# from np.core.numerictypes
self.assert_deprecated(lambda: np.typeDict)
def ExpandDims(inputs, axis=-1, **kwargs):
"""ExpandDims interface of NDArray.
Parameters
----------
inputs : Tensor
The input tensor.
axis : int
The insert position of new dimension. Default is ``-1`` (Push Back).
Returns
-------
Tensor
The output tensor.
Examples
--------
>>> a = Tensor(shape=[1, 2, 3, 4]).Variable()
>>> print ExpandDims(a).shape
>>> print ExpandDims(a, axis=2).shape
"""
CheckInputs(inputs, 1)
arguments = ParseArguments(locals())
output = Tensor.CreateOperator(nout=1, op_type='ExpandDims', **arguments)
if inputs.shape is not None:
output.shape = inputs.shape[:]
if axis == -1 or axis >= len(inputs.shape):
output.shape.append(np.long(1))
else:
output.shape.insert(axis, np.long(1))
return output
def metatimes_to_seconds_since_start(metatimes):
"""Convert metatime array to seconds since first datetime in array.
Inputs:
metatimes [np.array or pd.DatetimeIndex]: Array of metatimes.
metatimes are either:
np.array of datetime.datetime,
np.array of np.datetime64,
np.array of pd.Timestamp,
pd.DatetimeIndex.
Optional Inputs:
None.
Outputs:
seconds_since_start [np.array]: Array of long integers
indicating number of seconds since the first time in the arrray.
Optional Outputs:
None.
Example:
seconds_since_start = metatimes_to_seconds_since_start(metatimes)
"""
# Check type of input and do conversion accordingly
if isinstance(metatimes[0], datetime.datetime):
dt_since_start = metatimes - metatimes[0]
return np.array(
[np.long(metatime.total_seconds()) for metatime in dt_since_start])
elif isinstance(metatimes[0], np.datetime64 or pd.Timestamp):
npdts_since_start = metatimes - metatimes[0]
return np.array([
np.long(npdt_since_start / np.timedelta64(1, 's'))
for npdt_since_start in npdts_since_start
])
def apols(lin, amaxin):
# adapted from IDL procedure apols.pro written by Jesper Schou
l=np.long(lin)
amax=np.minimum(amaxin,2*l)
pols=np.zeros((2*l+1,amaxin+1))
# It is ESSENTIAL that x is set up such that x(-m)=-x(m) to full machine
# accuracy or that the re-orthogonalization is done with respect to all
# previous polynomials (second option below).
# x=(dindgen(2*l+1)-l)/l
x=np.linspace(-1,1,2*l+1)
pols[:,0]=1/np.sqrt(2*l+1.0)
if (amax >= 1):
pols[:,1]=x/np.sqrt((l+1.0)*(2*l+1.0)/(3.0*l))
# for n=2l,amax do begin
# Set up polynomials using exact recurrence relation.
for n in range(2,amax+1):
a0=2.0*l*(2*n-1.0)/(n*(2*l-n+1))
b0=-(n-1.0)/n*(2*l+n)/(2*l-n+1)
a=a0*np.sqrt((2*n+1.0)/(2*n-1.0)*(2*l-n+1.0)/(2*l+n+1.0))
b=b0*np.sqrt((2*n+1.0)/(2*n-3.0)*(2*l-n+1.0)*(2*l-n+2.0)/(2*l+n+1.0)/(2*l+n))
help=a*x*pols[:,n-1]+b*pols[:,n-2]
# Turns out that roundoff kills the algorithm, so we have to re-orthogonalize.
# Two choices here. First one is twice as fast and more accurate, but
# depends on the rounding being done in the standard IEEE way.
# for j=n-2,0,-2 do begin
for j in range(n-2,-1,-2):
# This choice is robust to the roundoff, but twice as slow and generally
# somewhat less accurate
# for j=n-1,0,-1 do begin
help=help-pols[:,j]*np.sum(help*pols[:,j])
# end
# Reset norm to 1.
pols[:,n]=help/np.sqrt(np.sum(np.square(help)))
# Reset polynomials to have P_l(l)=l by setting overall norm.
# Note that this results in more accurate overall normalization, but
# that P_l(l) may be very far from l. This is the key to the algorithm.
c=l**2*(2*l+1.0)
# for n=0l,amax do begin
for n in range(0,amax+1):
c=c*(2*l+n+1.0)/(2*l-n+1.0)
pols[:,n]=pols[:,n]*np.sqrt(c/(2*n+1))
return pols
def find_maximum_weight_graph(self):
vertices = {-1: 0, 0: 0, 1: self.data[0]}
for i in range(1, len(self.data)):
vertices[i] = np.long(
max(vertices[i - 1], vertices[i - 2] + self.data[i - 1]))
maximum_weight_graph = set()
position = len(self.data)
while position >= 1:
if vertices[position - 1] >= (vertices[position - 2] +
self.data[position - 1]):
position = position - 1
else:
maximum_weight_graph.add(position)
position = position - 2
self.maximum_weight_graph = maximum_weight_graph
return maximum_weight_graph
def sim_drift(v, V, a, z, Z, t, T, size=512, dt=1e-4, update=False, return_gpu=False):
global _generator, _out, _generators_per_block, _block_count
size = np.long(size)
if _generator is None or update:
_generator = pycuda.curandom.XORWOWRandomNumberGenerator()
_block_count = _generator.block_count
_generators_per_block = _generator.generators_per_block
if _out is None or update:
_out = gpuarray.empty(size, dtype=np.float32)
_sim_drift_cuda(_generator.state, np.float32(v), np.float32(V), np.float32(a), np.float32(z), np.float32(Z), np.float32(t), np.float32(T), np.float32(dt), np.float32(1), _out, np.uint32(size), block=(_generators_per_block, 1, 1), grid=(_block_count, 1))
if return_gpu:
return _out
else:
return _out.get()
def __init__(self, x_csv_file, y_csv_file):
self.x_scv_file_name = x_csv_file
self.y_scv_file_name = y_csv_file
self.len = 0
self.x_matrix = []
self.y_matrix = []
for line in open(self.x_scv_file_name):
self.len += 1
x = line.split(',')
x = [float(i) / 255 for i in x]
self.x_matrix.append(x)
for label in open(self.y_scv_file_name):
self.y_matrix.append(np.long(label))
self.x_matrix = np.array(self.x_matrix)
self.y_matrix = np.array(self.y_matrix)
pass
def __getitem__(self, index):
img = Image.open(self.img_path[index]).convert('RGB')
# img = ImageEnhance.Contrast(img)
# img.enhance(2.0) # 所有图片对比度调到2
if self.transform is not None:
img = self.transform(img)
# 原始SVHN中类别10为数字0
lbl = []
if len(self.img_label) > 0:
lbl = [np.long(x) for x in self.img_label[index]]
for i in range(4 - len(lbl)):
lbl.append(10) # 补齐4个字符，用10填充，定长字符识别
return img, torch.from_numpy(np.array(lbl)).long() # 这部分有问题
def _create_buffers(self, parallelism=5):
"""
Define the necessary input and ouptut Buffer objects for the Kernel,
store in self.input_buffers and self.output_buffers. Subclasses should
overwrite this.
"""
mf = cl.mem_flags
self.size = parallelism
parallelism = numpy.long(parallelism)
#self.buffers.append((parallelism,))
# local_size = cl.Buffer(self.ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=parallelism)
# self.buffers.append(local_size)
output = numpy.zeros(parallelism)
self.buffers.append(cl.Buffer(self.ctx, mf.WRITE_ONLY, output.nbytes))