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nwilming/ocupy
|
ocupy/simulator.py
|
makeHist
|
def makeHist(x_val, y_val, fit=spline_base.fit2d,
bins=[np.linspace(-36.5,36.5,74),np.linspace(-180,180,361)]):
"""
Constructs a (fitted) histogram of the given data.
Parameters:
x_val : array
The data to be histogrammed along the x-axis.
y_val : array
The data to be histogrammed along the y-axis.
fit : function or None, optional
The function to use in order to fit the data.
If no fit should be applied, set to None
bins : touple of arrays, giving the bin edges to be
used in the histogram. (First value: y-axis, Second value: x-axis)
"""
y_val = y_val[~np.isnan(y_val)]
x_val = x_val[~np.isnan(x_val)]
samples = list(zip(y_val, x_val))
K, xedges, yedges = np.histogram2d(y_val, x_val, bins=bins)
if (fit is None):
return K/ K.sum()
# Check if given attr is a function
elif hasattr(fit, '__call__'):
H = fit(np.array(samples), bins[0], bins[1], p_est=K)[0]
return H/H.sum()
else:
raise TypeError("Not a valid argument, insert spline function or None")
|
python
|
def makeHist(x_val, y_val, fit=spline_base.fit2d,
bins=[np.linspace(-36.5,36.5,74),np.linspace(-180,180,361)]):
"""
Constructs a (fitted) histogram of the given data.
Parameters:
x_val : array
The data to be histogrammed along the x-axis.
y_val : array
The data to be histogrammed along the y-axis.
fit : function or None, optional
The function to use in order to fit the data.
If no fit should be applied, set to None
bins : touple of arrays, giving the bin edges to be
used in the histogram. (First value: y-axis, Second value: x-axis)
"""
y_val = y_val[~np.isnan(y_val)]
x_val = x_val[~np.isnan(x_val)]
samples = list(zip(y_val, x_val))
K, xedges, yedges = np.histogram2d(y_val, x_val, bins=bins)
if (fit is None):
return K/ K.sum()
# Check if given attr is a function
elif hasattr(fit, '__call__'):
H = fit(np.array(samples), bins[0], bins[1], p_est=K)[0]
return H/H.sum()
else:
raise TypeError("Not a valid argument, insert spline function or None")
|
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y_val : array
The data to be histogrammed along the y-axis.
fit : function or None, optional
The function to use in order to fit the data.
If no fit should be applied, set to None
bins : touple of arrays, giving the bin edges to be
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|
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train
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https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L374-L405
|
nwilming/ocupy
|
ocupy/simulator.py
|
firstSacDist
|
def firstSacDist(fm):
"""
Computes the distribution of angle and length
combinations that were made as first saccades
Parameters:
fm : ocupy.fixmat
The fixation data to be analysed
"""
ang, leng, ad, ld = anglendiff(fm, return_abs=True)
y_arg = leng[0][np.roll(fm.fix == min(fm.fix), 1)]/fm.pixels_per_degree
x_arg = reshift(ang[0][np.roll(fm.fix == min(fm.fix), 1)])
bins = [list(range(int(ceil(np.nanmax(y_arg)))+1)), np.linspace(-180, 180, 361)]
return makeHist(x_arg, y_arg, fit=None, bins = bins)
|
python
|
def firstSacDist(fm):
"""
Computes the distribution of angle and length
combinations that were made as first saccades
Parameters:
fm : ocupy.fixmat
The fixation data to be analysed
"""
ang, leng, ad, ld = anglendiff(fm, return_abs=True)
y_arg = leng[0][np.roll(fm.fix == min(fm.fix), 1)]/fm.pixels_per_degree
x_arg = reshift(ang[0][np.roll(fm.fix == min(fm.fix), 1)])
bins = [list(range(int(ceil(np.nanmax(y_arg)))+1)), np.linspace(-180, 180, 361)]
return makeHist(x_arg, y_arg, fit=None, bins = bins)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L509-L523
|
nwilming/ocupy
|
ocupy/simulator.py
|
trajLenDist
|
def trajLenDist(fm):
"""
Computes the distribution of trajectory lengths, i.e.
the number of saccades that were made as a part of one trajectory
Parameters:
fm : ocupy.fixmat
The fixation data to be analysed
"""
trajLen = np.roll(fm.fix, 1)[fm.fix == min(fm.fix)]
val, borders = np.histogram(trajLen,
bins=np.linspace(-0.5, max(trajLen)+0.5, max(trajLen)+2))
cumsum = np.cumsum(val.astype(float) / val.sum())
return cumsum, borders
|
python
|
def trajLenDist(fm):
"""
Computes the distribution of trajectory lengths, i.e.
the number of saccades that were made as a part of one trajectory
Parameters:
fm : ocupy.fixmat
The fixation data to be analysed
"""
trajLen = np.roll(fm.fix, 1)[fm.fix == min(fm.fix)]
val, borders = np.histogram(trajLen,
bins=np.linspace(-0.5, max(trajLen)+0.5, max(trajLen)+2))
cumsum = np.cumsum(val.astype(float) / val.sum())
return cumsum, borders
|
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https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L525-L539
|
nwilming/ocupy
|
ocupy/simulator.py
|
reshift
|
def reshift(I):
"""
Transforms the given number element into a range of [-180, 180],
which covers all possible angle differences. This method reshifts larger or
smaller numbers that might be the output of other angular calculations
into that range by adding or subtracting 360, respectively.
To make sure that angular data ranges between -180 and 180 in order to be
properly histogrammed, apply this method first.
Parameters:
I : array or list or int or float
Number or numbers that shall be reshifted.
Farell, Ludwig, Ellis, and Gilchrist
Returns:
numpy.ndarray : Reshifted number or numbers as array
"""
# Output -180 to +180
if type(I)==list:
I = np.array(I)
return ((I-180)%360)-180
|
python
|
def reshift(I):
"""
Transforms the given number element into a range of [-180, 180],
which covers all possible angle differences. This method reshifts larger or
smaller numbers that might be the output of other angular calculations
into that range by adding or subtracting 360, respectively.
To make sure that angular data ranges between -180 and 180 in order to be
properly histogrammed, apply this method first.
Parameters:
I : array or list or int or float
Number or numbers that shall be reshifted.
Farell, Ludwig, Ellis, and Gilchrist
Returns:
numpy.ndarray : Reshifted number or numbers as array
"""
# Output -180 to +180
if type(I)==list:
I = np.array(I)
return ((I-180)%360)-180
|
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To make sure that angular data ranges between -180 and 180 in order to be
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Number or numbers that shall be reshifted.
Farell, Ludwig, Ellis, and Gilchrist
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L541-L562
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen.initializeData
|
def initializeData(self, fit = None, full_H1=None, max_length = 40,
in_deg = True):
"""
Prepares the data to be replicated. Calculates the second-order length
and angle dependencies between saccades and stores them in a fitted
histogram.
Parameters:
fit : function, optional
The method to use for fitting the histogram
full_H1 : twodimensional numpy.ndarray, optional
Where applicable, the distribution of angle and length
differences to replicate with dimensions [73,361]
"""
a, l, ad, ld = anglendiff(self.fm, roll=1, return_abs = True)
if in_deg:
self.fm.pixels_per_degree = 1
samples = np.zeros([3, len(l[0])])
samples[0] = l[0]/self.fm.pixels_per_degree
samples[1] = np.roll(l[0]/self.fm.pixels_per_degree,-1)
samples[2] = np.roll(reshift(ad[0]),-1)
z = np.any(np.isnan(samples), axis=0)
samples = samples[:,~np.isnan(samples).any(0)]
if full_H1 is None:
self.full_H1 = []
for i in range(1, int(ceil(max_length+1))):
idx = np.logical_and(samples[0]<=i, samples[0]>i-1)
if idx.any():
self.full_H1.append(makeHist(samples[2][idx], samples[1][idx], fit=fit,
bins=[np.linspace(0,max_length-1,max_length),np.linspace(-180,180,361)]))
# Sometimes if there's only one sample present there seems to occur a problem
# with histogram calculation and the hist is filled with nans. In this case, dismiss
# the hist.
if np.isnan(self.full_H1[-1]).any():
self.full_H1[-1] = np.array([])
self.nosamples.append(len(samples[2][idx]))
else:
self.full_H1.append(np.array([]))
self.nosamples.append(0)
else:
self.full_H1 = full_H1
self.firstLenAng_cumsum, self.firstLenAng_shape = (
compute_cumsum(firstSacDist(self.fm)))
self.probability_cumsum = []
for i in range(len(self.full_H1)):
if self.full_H1[i] == []:
self.probability_cumsum.append(np.array([]))
else:
self.probability_cumsum.append(np.cumsum(self.full_H1[i].flat))
self.trajLen_cumsum, self.trajLen_borders = trajLenDist(self.fm)
min_distance = 1/np.array([min((np.unique(self.probability_cumsum[i]) \
-np.roll(np.unique(self.probability_cumsum[i]),1))[1:]) \
for i in range(len(self.probability_cumsum))])
# Set a minimal resolution
min_distance[min_distance<10] = 10
self.linind = {}
for i in range(len(self.probability_cumsum)):
self.linind['self.probability_cumsum '+repr(i)] = np.linspace(0,1,min_distance[i])[0:-1]
for elem in [self.firstLenAng_cumsum, self.trajLen_cumsum]:
self.linind[elem] = np.linspace(0, 1, 1/min((np.unique((elem))-np.roll(np.unique((elem)),1))[1:]))[0:-1]
|
python
|
def initializeData(self, fit = None, full_H1=None, max_length = 40,
in_deg = True):
"""
Prepares the data to be replicated. Calculates the second-order length
and angle dependencies between saccades and stores them in a fitted
histogram.
Parameters:
fit : function, optional
The method to use for fitting the histogram
full_H1 : twodimensional numpy.ndarray, optional
Where applicable, the distribution of angle and length
differences to replicate with dimensions [73,361]
"""
a, l, ad, ld = anglendiff(self.fm, roll=1, return_abs = True)
if in_deg:
self.fm.pixels_per_degree = 1
samples = np.zeros([3, len(l[0])])
samples[0] = l[0]/self.fm.pixels_per_degree
samples[1] = np.roll(l[0]/self.fm.pixels_per_degree,-1)
samples[2] = np.roll(reshift(ad[0]),-1)
z = np.any(np.isnan(samples), axis=0)
samples = samples[:,~np.isnan(samples).any(0)]
if full_H1 is None:
self.full_H1 = []
for i in range(1, int(ceil(max_length+1))):
idx = np.logical_and(samples[0]<=i, samples[0]>i-1)
if idx.any():
self.full_H1.append(makeHist(samples[2][idx], samples[1][idx], fit=fit,
bins=[np.linspace(0,max_length-1,max_length),np.linspace(-180,180,361)]))
# Sometimes if there's only one sample present there seems to occur a problem
# with histogram calculation and the hist is filled with nans. In this case, dismiss
# the hist.
if np.isnan(self.full_H1[-1]).any():
self.full_H1[-1] = np.array([])
self.nosamples.append(len(samples[2][idx]))
else:
self.full_H1.append(np.array([]))
self.nosamples.append(0)
else:
self.full_H1 = full_H1
self.firstLenAng_cumsum, self.firstLenAng_shape = (
compute_cumsum(firstSacDist(self.fm)))
self.probability_cumsum = []
for i in range(len(self.full_H1)):
if self.full_H1[i] == []:
self.probability_cumsum.append(np.array([]))
else:
self.probability_cumsum.append(np.cumsum(self.full_H1[i].flat))
self.trajLen_cumsum, self.trajLen_borders = trajLenDist(self.fm)
min_distance = 1/np.array([min((np.unique(self.probability_cumsum[i]) \
-np.roll(np.unique(self.probability_cumsum[i]),1))[1:]) \
for i in range(len(self.probability_cumsum))])
# Set a minimal resolution
min_distance[min_distance<10] = 10
self.linind = {}
for i in range(len(self.probability_cumsum)):
self.linind['self.probability_cumsum '+repr(i)] = np.linspace(0,1,min_distance[i])[0:-1]
for elem in [self.firstLenAng_cumsum, self.trajLen_cumsum]:
self.linind[elem] = np.linspace(0, 1, 1/min((np.unique((elem))-np.roll(np.unique((elem)),1))[1:]))[0:-1]
|
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Prepares the data to be replicated. Calculates the second-order length
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Parameters:
fit : function, optional
The method to use for fitting the histogram
full_H1 : twodimensional numpy.ndarray, optional
Where applicable, the distribution of angle and length
differences to replicate with dimensions [73,361]
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L90-L157
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen._calc_xy
|
def _calc_xy(self, xxx_todo_changeme, angle, length):
"""
Calculates the coordinates after a specific saccade was made.
Parameters:
(x,y) : tuple of floats or ints
The coordinates before the saccade was made
angle : float or int
The angle that the next saccade encloses with the
horizontal display border
length: float or int
The length of the next saccade
"""
(x, y) = xxx_todo_changeme
return (x+(cos(radians(angle))*length),
y+(sin(radians(angle))*length))
|
python
|
def _calc_xy(self, xxx_todo_changeme, angle, length):
"""
Calculates the coordinates after a specific saccade was made.
Parameters:
(x,y) : tuple of floats or ints
The coordinates before the saccade was made
angle : float or int
The angle that the next saccade encloses with the
horizontal display border
length: float or int
The length of the next saccade
"""
(x, y) = xxx_todo_changeme
return (x+(cos(radians(angle))*length),
y+(sin(radians(angle))*length))
|
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The coordinates before the saccade was made
angle : float or int
The angle that the next saccade encloses with the
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length: float or int
The length of the next saccade
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L159-L174
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen._draw
|
def _draw(self, prev_angle = None, prev_length = None):
"""
Draws a new length- and angle-difference pair and calculates
length and angle absolutes matching the last saccade drawn.
Parameters:
prev_angle : float, optional
The last angle that was drawn in the current trajectory
prev_length : float, optional
The last length that was drawn in the current trajectory
Note: Either both prev_angle and prev_length have to be given
or none; if only one parameter is given, it will be neglected.
"""
if (prev_angle is None) or (prev_length is None):
(length, angle)= np.unravel_index(self.drawFrom('self.firstLenAng_cumsum', self.getrand('self.firstLenAng_cumsum')),
self.firstLenAng_shape)
angle = angle-((self.firstLenAng_shape[1]-1)/2)
angle += 0.5
length += 0.5
length *= self.fm.pixels_per_degree
else:
ind = int(floor(prev_length/self.fm.pixels_per_degree))
while ind >= len(self.probability_cumsum):
ind -= 1
while not(self.probability_cumsum[ind]).any():
ind -= 1
J, I = np.unravel_index(self.drawFrom('self.probability_cumsum '+repr(ind),self.getrand('self.probability_cumsum '+repr(ind))),
self.full_H1[ind].shape)
angle = reshift((I-self.full_H1[ind].shape[1]/2) + prev_angle)
angle += 0.5
length = J+0.5
length *= self.fm.pixels_per_degree
return angle, length
|
python
|
def _draw(self, prev_angle = None, prev_length = None):
"""
Draws a new length- and angle-difference pair and calculates
length and angle absolutes matching the last saccade drawn.
Parameters:
prev_angle : float, optional
The last angle that was drawn in the current trajectory
prev_length : float, optional
The last length that was drawn in the current trajectory
Note: Either both prev_angle and prev_length have to be given
or none; if only one parameter is given, it will be neglected.
"""
if (prev_angle is None) or (prev_length is None):
(length, angle)= np.unravel_index(self.drawFrom('self.firstLenAng_cumsum', self.getrand('self.firstLenAng_cumsum')),
self.firstLenAng_shape)
angle = angle-((self.firstLenAng_shape[1]-1)/2)
angle += 0.5
length += 0.5
length *= self.fm.pixels_per_degree
else:
ind = int(floor(prev_length/self.fm.pixels_per_degree))
while ind >= len(self.probability_cumsum):
ind -= 1
while not(self.probability_cumsum[ind]).any():
ind -= 1
J, I = np.unravel_index(self.drawFrom('self.probability_cumsum '+repr(ind),self.getrand('self.probability_cumsum '+repr(ind))),
self.full_H1[ind].shape)
angle = reshift((I-self.full_H1[ind].shape[1]/2) + prev_angle)
angle += 0.5
length = J+0.5
length *= self.fm.pixels_per_degree
return angle, length
|
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Draws a new length- and angle-difference pair and calculates
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The last angle that was drawn in the current trajectory
prev_length : float, optional
The last length that was drawn in the current trajectory
Note: Either both prev_angle and prev_length have to be given
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L176-L212
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen.sample_many
|
def sample_many(self, num_samples = 2000):
"""
Generates a given number of trajectories, using the method sample().
Returns a fixmat with the generated data.
Parameters:
num_samples : int, optional
The number of trajectories that shall be generated.
"""
x = []
y = []
fix = []
sample = []
# XXX: Delete ProgressBar
pbar = ProgressBar(widgets=[Percentage(),Bar()], maxval=num_samples).start()
for s in range(0, num_samples):
for i, (xs, ys) in enumerate(self.sample()):
x.append(xs)
y.append(ys)
fix.append(i+1)
sample.append(s)
pbar.update(s+1)
fields = {'fix':np.array(fix), 'y':np.array(y), 'x':np.array(x)}
param = {'pixels_per_degree':self.fm.pixels_per_degree}
out = fixmat.VectorFixmatFactory(fields, param)
return out
|
python
|
def sample_many(self, num_samples = 2000):
"""
Generates a given number of trajectories, using the method sample().
Returns a fixmat with the generated data.
Parameters:
num_samples : int, optional
The number of trajectories that shall be generated.
"""
x = []
y = []
fix = []
sample = []
# XXX: Delete ProgressBar
pbar = ProgressBar(widgets=[Percentage(),Bar()], maxval=num_samples).start()
for s in range(0, num_samples):
for i, (xs, ys) in enumerate(self.sample()):
x.append(xs)
y.append(ys)
fix.append(i+1)
sample.append(s)
pbar.update(s+1)
fields = {'fix':np.array(fix), 'y':np.array(y), 'x':np.array(x)}
param = {'pixels_per_degree':self.fm.pixels_per_degree}
out = fixmat.VectorFixmatFactory(fields, param)
return out
|
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Returns a fixmat with the generated data.
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L241-L269
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen.sample
|
def sample(self):
"""
Draws a trajectory length, first coordinates, lengths, angles and
length-angle-difference pairs according to the empirical distribution.
Each call creates one complete trajectory.
"""
lenghts = []
angles = []
coordinates = []
fix = []
sample_size = int(round(self.trajLen_borders[self.drawFrom('self.trajLen_cumsum', self.getrand('self.trajLen_cumsum'))]))
coordinates.append([0, 0])
fix.append(1)
while len(coordinates) < sample_size:
if len(lenghts) == 0 and len(angles) == 0:
angle, length = self._draw(self)
else:
angle, length = self._draw(prev_angle = angles[-1],
prev_length = lenghts[-1])
x, y = self._calc_xy(coordinates[-1], angle, length)
coordinates.append([x, y])
lenghts.append(length)
angles.append(angle)
fix.append(fix[-1]+1)
return coordinates
|
python
|
def sample(self):
"""
Draws a trajectory length, first coordinates, lengths, angles and
length-angle-difference pairs according to the empirical distribution.
Each call creates one complete trajectory.
"""
lenghts = []
angles = []
coordinates = []
fix = []
sample_size = int(round(self.trajLen_borders[self.drawFrom('self.trajLen_cumsum', self.getrand('self.trajLen_cumsum'))]))
coordinates.append([0, 0])
fix.append(1)
while len(coordinates) < sample_size:
if len(lenghts) == 0 and len(angles) == 0:
angle, length = self._draw(self)
else:
angle, length = self._draw(prev_angle = angles[-1],
prev_length = lenghts[-1])
x, y = self._calc_xy(coordinates[-1], angle, length)
coordinates.append([x, y])
lenghts.append(length)
angles.append(angle)
fix.append(fix[-1]+1)
return coordinates
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L271-L299
|
nwilming/ocupy
|
ocupy/simulator.py
|
FixGen.drawFrom
|
def drawFrom(self, cumsum, r):
"""
Draws a value from a cumulative sum.
Parameters:
cumsum : array
Cumulative sum from which shall be drawn.
Returns:
int : Index of the cumulative sum element drawn.
"""
a = cumsum.rsplit()
if len(a)>1:
b = eval(a[0])[int(a[1])]
else:
b = eval(a[0])
return np.nonzero(b>=r)[0][0]
|
python
|
def drawFrom(self, cumsum, r):
"""
Draws a value from a cumulative sum.
Parameters:
cumsum : array
Cumulative sum from which shall be drawn.
Returns:
int : Index of the cumulative sum element drawn.
"""
a = cumsum.rsplit()
if len(a)>1:
b = eval(a[0])[int(a[1])]
else:
b = eval(a[0])
return np.nonzero(b>=r)[0][0]
|
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Draws a value from a cumulative sum.
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/simulator.py#L305-L322
|
nwilming/ocupy
|
ocupy/fixmat.py
|
load
|
def load(path):
"""
Load fixmat at path.
Parameters:
path : string
Absolute path of the file to load from.
"""
f = h5py.File(path,'r')
if 'Fixmat' in f:
fm_group = f['Fixmat']
else:
fm_group = f['Datamat']
fields = {}
params = {}
for field, value in list(fm_group.items()):
fields[field] = np.array(value)
for param, value in list(fm_group.attrs.items()):
params[param] = value
f.close()
return VectorFixmatFactory(fields, params)
|
python
|
def load(path):
"""
Load fixmat at path.
Parameters:
path : string
Absolute path of the file to load from.
"""
f = h5py.File(path,'r')
if 'Fixmat' in f:
fm_group = f['Fixmat']
else:
fm_group = f['Datamat']
fields = {}
params = {}
for field, value in list(fm_group.items()):
fields[field] = np.array(value)
for param, value in list(fm_group.attrs.items()):
params[param] = value
f.close()
return VectorFixmatFactory(fields, params)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L140-L160
|
nwilming/ocupy
|
ocupy/fixmat.py
|
compute_fdm
|
def compute_fdm(fixmat, fwhm=2, scale_factor=1):
"""
Computes a fixation density map for the calling fixmat.
Creates a map the size of the image fixations were recorded on.
Every pixel contains the frequency of fixations
for this image. The fixation map is smoothed by convolution with a
Gaussian kernel to approximate the area with highest processing
(usually 2 deg. visual angle).
Note: The function does not check whether the fixmat contains
fixations from different images as it might be desirable to compute
fdms over fixations from more than one image.
Parameters:
fwhm : float
the full width at half maximum of the Gaussian kernel used
for convolution of the fixation frequency map.
scale_factor : float
scale factor for the resulting fdm. Default is 1. Scale_factor
must be a float specifying the fraction of the current size.
Returns:
fdm : numpy.array
a numpy.array of size fixmat.image_size containing
the fixation probability for every location on the image.
"""
# image category must exist (>-1) and image_size must be non-empty
assert (len(fixmat.image_size) == 2 and (fixmat.image_size[0] > 0) and
(fixmat.image_size[1] > 0)), 'The image_size is either 0, or not 2D'
# check whether fixmat contains fixations
if fixmat._num_fix == 0 or len(fixmat.x) == 0 or len(fixmat.y) == 0 :
raise RuntimeError('There are no fixations in the fixmat.')
assert not scale_factor <= 0, "scale_factor has to be > 0"
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
e_y = np.arange(0, np.round(scale_factor*fixmat.image_size[0]+1))
e_x = np.arange(0, np.round(scale_factor*fixmat.image_size[1]+1))
samples = np.array(list(zip((scale_factor*fixmat.y), (scale_factor*fixmat.x))))
(hist, _) = np.histogramdd(samples, (e_y, e_x))
kernel_sigma = fwhm * fixmat.pixels_per_degree * scale_factor
kernel_sigma = kernel_sigma / (2 * (2 * np.log(2)) ** .5)
fdm = gaussian_filter(hist, kernel_sigma, order=0, mode='constant')
return fdm / fdm.sum()
|
python
|
def compute_fdm(fixmat, fwhm=2, scale_factor=1):
"""
Computes a fixation density map for the calling fixmat.
Creates a map the size of the image fixations were recorded on.
Every pixel contains the frequency of fixations
for this image. The fixation map is smoothed by convolution with a
Gaussian kernel to approximate the area with highest processing
(usually 2 deg. visual angle).
Note: The function does not check whether the fixmat contains
fixations from different images as it might be desirable to compute
fdms over fixations from more than one image.
Parameters:
fwhm : float
the full width at half maximum of the Gaussian kernel used
for convolution of the fixation frequency map.
scale_factor : float
scale factor for the resulting fdm. Default is 1. Scale_factor
must be a float specifying the fraction of the current size.
Returns:
fdm : numpy.array
a numpy.array of size fixmat.image_size containing
the fixation probability for every location on the image.
"""
# image category must exist (>-1) and image_size must be non-empty
assert (len(fixmat.image_size) == 2 and (fixmat.image_size[0] > 0) and
(fixmat.image_size[1] > 0)), 'The image_size is either 0, or not 2D'
# check whether fixmat contains fixations
if fixmat._num_fix == 0 or len(fixmat.x) == 0 or len(fixmat.y) == 0 :
raise RuntimeError('There are no fixations in the fixmat.')
assert not scale_factor <= 0, "scale_factor has to be > 0"
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
e_y = np.arange(0, np.round(scale_factor*fixmat.image_size[0]+1))
e_x = np.arange(0, np.round(scale_factor*fixmat.image_size[1]+1))
samples = np.array(list(zip((scale_factor*fixmat.y), (scale_factor*fixmat.x))))
(hist, _) = np.histogramdd(samples, (e_y, e_x))
kernel_sigma = fwhm * fixmat.pixels_per_degree * scale_factor
kernel_sigma = kernel_sigma / (2 * (2 * np.log(2)) ** .5)
fdm = gaussian_filter(hist, kernel_sigma, order=0, mode='constant')
return fdm / fdm.sum()
|
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Gaussian kernel to approximate the area with highest processing
(usually 2 deg. visual angle).
Note: The function does not check whether the fixmat contains
fixations from different images as it might be desirable to compute
fdms over fixations from more than one image.
Parameters:
fwhm : float
the full width at half maximum of the Gaussian kernel used
for convolution of the fixation frequency map.
scale_factor : float
scale factor for the resulting fdm. Default is 1. Scale_factor
must be a float specifying the fraction of the current size.
Returns:
fdm : numpy.array
a numpy.array of size fixmat.image_size containing
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L163-L207
|
nwilming/ocupy
|
ocupy/fixmat.py
|
relative_bias
|
def relative_bias(fm, scale_factor = 1, estimator = None):
"""
Computes the relative bias, i.e. the distribution of saccade angles
and amplitudes.
Parameters:
fm : DataMat
The fixation data to use
scale_factor : double
Returns:
2D probability distribution of saccade angles and amplitudes.
"""
assert 'fix' in fm.fieldnames(), "Can not work without fixation numbers"
excl = fm.fix - np.roll(fm.fix, 1) != 1
# Now calculate the direction where the NEXT fixation goes to
diff_x = (np.roll(fm.x, 1) - fm.x)[~excl]
diff_y = (np.roll(fm.y, 1) - fm.y)[~excl]
# Make a histogram of diff values
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
ylim = np.round(scale_factor * fm.image_size[0])
xlim = np.round(scale_factor * fm.image_size[1])
x_steps = np.ceil(2*xlim) +1
if x_steps % 2 != 0: x_steps+=1
y_steps = np.ceil(2*ylim)+1
if y_steps % 2 != 0: y_steps+=1
e_x = np.linspace(-xlim,xlim,x_steps)
e_y = np.linspace(-ylim,ylim,y_steps)
#e_y = np.arange(-ylim, ylim+1)
#e_x = np.arange(-xlim, xlim+1)
samples = np.array(list(zip((scale_factor * diff_y),
(scale_factor* diff_x))))
if estimator == None:
(hist, _) = np.histogramdd(samples, (e_y, e_x))
else:
hist = estimator(samples, e_y, e_x)
return hist
|
python
|
def relative_bias(fm, scale_factor = 1, estimator = None):
"""
Computes the relative bias, i.e. the distribution of saccade angles
and amplitudes.
Parameters:
fm : DataMat
The fixation data to use
scale_factor : double
Returns:
2D probability distribution of saccade angles and amplitudes.
"""
assert 'fix' in fm.fieldnames(), "Can not work without fixation numbers"
excl = fm.fix - np.roll(fm.fix, 1) != 1
# Now calculate the direction where the NEXT fixation goes to
diff_x = (np.roll(fm.x, 1) - fm.x)[~excl]
diff_y = (np.roll(fm.y, 1) - fm.y)[~excl]
# Make a histogram of diff values
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
ylim = np.round(scale_factor * fm.image_size[0])
xlim = np.round(scale_factor * fm.image_size[1])
x_steps = np.ceil(2*xlim) +1
if x_steps % 2 != 0: x_steps+=1
y_steps = np.ceil(2*ylim)+1
if y_steps % 2 != 0: y_steps+=1
e_x = np.linspace(-xlim,xlim,x_steps)
e_y = np.linspace(-ylim,ylim,y_steps)
#e_y = np.arange(-ylim, ylim+1)
#e_x = np.arange(-xlim, xlim+1)
samples = np.array(list(zip((scale_factor * diff_y),
(scale_factor* diff_x))))
if estimator == None:
(hist, _) = np.histogramdd(samples, (e_y, e_x))
else:
hist = estimator(samples, e_y, e_x)
return hist
|
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fm : DataMat
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2D probability distribution of saccade angles and amplitudes.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L209-L249
|
nwilming/ocupy
|
ocupy/fixmat.py
|
DirectoryFixmatFactory
|
def DirectoryFixmatFactory(directory, categories = None, glob_str = '*.mat', var_name = 'fixmat'):
"""
Concatenates all fixmats in dir and returns the resulting single
fixmat.
Parameters:
directory : string
Path from which the fixmats should be loaded
categories : instance of stimuli.Categories, optional
If given, the resulting fixmat provides direct access
to the data in the categories object.
glob_str : string
A regular expression that defines which mat files are picked up.
var_name : string
The variable to load from the mat file.
Returns:
f_all : instance of FixMat
Contains all fixmats that were found in given directory
"""
files = glob(join(directory,glob_str))
if len(files) == 0:
raise ValueError("Could not find any fixmats in " +
join(directory, glob_str))
f_all = FixmatFactory(files.pop(), categories, var_name)
for fname in files:
f_current = FixmatFactory(fname, categories, var_name)
f_all.join(f_current)
return f_all
|
python
|
def DirectoryFixmatFactory(directory, categories = None, glob_str = '*.mat', var_name = 'fixmat'):
"""
Concatenates all fixmats in dir and returns the resulting single
fixmat.
Parameters:
directory : string
Path from which the fixmats should be loaded
categories : instance of stimuli.Categories, optional
If given, the resulting fixmat provides direct access
to the data in the categories object.
glob_str : string
A regular expression that defines which mat files are picked up.
var_name : string
The variable to load from the mat file.
Returns:
f_all : instance of FixMat
Contains all fixmats that were found in given directory
"""
files = glob(join(directory,glob_str))
if len(files) == 0:
raise ValueError("Could not find any fixmats in " +
join(directory, glob_str))
f_all = FixmatFactory(files.pop(), categories, var_name)
for fname in files:
f_current = FixmatFactory(fname, categories, var_name)
f_all.join(f_current)
return f_all
|
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Concatenates all fixmats in dir and returns the resulting single
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Path from which the fixmats should be loaded
categories : instance of stimuli.Categories, optional
If given, the resulting fixmat provides direct access
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glob_str : string
A regular expression that defines which mat files are picked up.
var_name : string
The variable to load from the mat file.
Returns:
f_all : instance of FixMat
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L252-L280
|
nwilming/ocupy
|
ocupy/fixmat.py
|
FixmatFactory
|
def FixmatFactory(fixmatfile, categories = None, var_name = 'fixmat', field_name='x'):
"""
Loads a single fixmat (fixmatfile).
Parameters:
fixmatfile : string
The matlab fixmat that should be loaded.
categories : instance of stimuli.Categories, optional
Links data in categories to data in fixmat.
"""
try:
data = loadmat(fixmatfile, struct_as_record = False)
keys = list(data.keys())
data = data[var_name][0][0]
except KeyError:
raise RuntimeError('%s is not a field of the matlab structure. Possible'+
'Keys are %s'%str(keys))
num_fix = data.__getattribute__(field_name).size
# Get a list with fieldnames and a list with parameters
fields = {}
parameters = {}
for field in data._fieldnames:
if data.__getattribute__(field).size == num_fix:
fields[field] = data.__getattribute__(field)
else:
parameters[field] = data.__getattribute__(field)[0].tolist()
if len(parameters[field]) == 1:
parameters[field] = parameters[field][0]
# Generate FixMat
fixmat = FixMat(categories = categories)
fixmat._fields = list(fields.keys())
for (field, value) in list(fields.items()):
fixmat.__dict__[field] = value.reshape(-1,)
fixmat._parameters = parameters
fixmat._subjects = None
for (field, value) in list(parameters.items()):
fixmat.__dict__[field] = value
fixmat._num_fix = num_fix
return fixmat
|
python
|
def FixmatFactory(fixmatfile, categories = None, var_name = 'fixmat', field_name='x'):
"""
Loads a single fixmat (fixmatfile).
Parameters:
fixmatfile : string
The matlab fixmat that should be loaded.
categories : instance of stimuli.Categories, optional
Links data in categories to data in fixmat.
"""
try:
data = loadmat(fixmatfile, struct_as_record = False)
keys = list(data.keys())
data = data[var_name][0][0]
except KeyError:
raise RuntimeError('%s is not a field of the matlab structure. Possible'+
'Keys are %s'%str(keys))
num_fix = data.__getattribute__(field_name).size
# Get a list with fieldnames and a list with parameters
fields = {}
parameters = {}
for field in data._fieldnames:
if data.__getattribute__(field).size == num_fix:
fields[field] = data.__getattribute__(field)
else:
parameters[field] = data.__getattribute__(field)[0].tolist()
if len(parameters[field]) == 1:
parameters[field] = parameters[field][0]
# Generate FixMat
fixmat = FixMat(categories = categories)
fixmat._fields = list(fields.keys())
for (field, value) in list(fields.items()):
fixmat.__dict__[field] = value.reshape(-1,)
fixmat._parameters = parameters
fixmat._subjects = None
for (field, value) in list(parameters.items()):
fixmat.__dict__[field] = value
fixmat._num_fix = num_fix
return fixmat
|
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Loads a single fixmat (fixmatfile).
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L283-L325
|
nwilming/ocupy
|
ocupy/fixmat.py
|
FixMat.add_feature_values
|
def add_feature_values(self, features):
"""
Adds feature values of feature 'feature' to all fixations in
the calling fixmat.
For fixations out of the image boundaries, NaNs are returned.
The function generates a new attribute field named with the
string in features that contains an np.array listing feature
values for every fixation in the fixmat.
.. note:: The calling fixmat must have been constructed with an
stimuli.Categories object
Parameters:
features : string
list of feature names for which feature values are extracted.
"""
if not 'x' in self.fieldnames():
raise RuntimeError("""add_feature_values expects to find
(x,y) locations in self.x and self.y. But self.x does not exist""")
if not self._categories:
raise RuntimeError(
'''"%s" does not exist as a fieldname and the
fixmat does not have a Categories object (no features
available. The fixmat has these fields: %s''' \
%(features, str(self._fields)))
for feature in features:
# initialize new field with NaNs
feat_vals = np.zeros([len(self.x)]) * np.nan
for (cat_mat, imgs) in self.by_cat():
for img in np.unique(cat_mat.filenumber).astype(int):
fmap = imgs[img][feature]
on_image = (self.x >= 0) & (self.x <= self.image_size[1])
on_image = on_image & (self.y >= 0) & (self.y <= self.image_size[0])
idx = (self.category == imgs.category) & \
(self.filenumber == img) & \
(on_image.astype('bool'))
feat_vals[idx] = fmap[self.y[idx].astype('int'),
self.x[idx].astype('int')]
# setattr(self, feature, feat_vals)
self.add_field(feature, feat_vals)
|
python
|
def add_feature_values(self, features):
"""
Adds feature values of feature 'feature' to all fixations in
the calling fixmat.
For fixations out of the image boundaries, NaNs are returned.
The function generates a new attribute field named with the
string in features that contains an np.array listing feature
values for every fixation in the fixmat.
.. note:: The calling fixmat must have been constructed with an
stimuli.Categories object
Parameters:
features : string
list of feature names for which feature values are extracted.
"""
if not 'x' in self.fieldnames():
raise RuntimeError("""add_feature_values expects to find
(x,y) locations in self.x and self.y. But self.x does not exist""")
if not self._categories:
raise RuntimeError(
'''"%s" does not exist as a fieldname and the
fixmat does not have a Categories object (no features
available. The fixmat has these fields: %s''' \
%(features, str(self._fields)))
for feature in features:
# initialize new field with NaNs
feat_vals = np.zeros([len(self.x)]) * np.nan
for (cat_mat, imgs) in self.by_cat():
for img in np.unique(cat_mat.filenumber).astype(int):
fmap = imgs[img][feature]
on_image = (self.x >= 0) & (self.x <= self.image_size[1])
on_image = on_image & (self.y >= 0) & (self.y <= self.image_size[0])
idx = (self.category == imgs.category) & \
(self.filenumber == img) & \
(on_image.astype('bool'))
feat_vals[idx] = fmap[self.y[idx].astype('int'),
self.x[idx].astype('int')]
# setattr(self, feature, feat_vals)
self.add_field(feature, feat_vals)
|
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Adds feature values of feature 'feature' to all fixations in
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For fixations out of the image boundaries, NaNs are returned.
The function generates a new attribute field named with the
string in features that contains an np.array listing feature
values for every fixation in the fixmat.
.. note:: The calling fixmat must have been constructed with an
stimuli.Categories object
Parameters:
features : string
list of feature names for which feature values are extracted.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L19-L60
|
nwilming/ocupy
|
ocupy/fixmat.py
|
FixMat.make_reg_data
|
def make_reg_data(self, feature_list=None, all_controls=False):
"""
Generates two M x N matrices with M feature values at fixations for
N features. Controls are a random sample out of all non-fixated regions
of an image or fixations of the same subject group on a randomly chosen
image. Fixations are pooled over all subjects in the calling fixmat.
Parameters :
all_controls : bool
if True, all non-fixated points on a feature map are takes as
control values. If False, controls are fixations from the same
subjects but on one other randomly chosen image of the same
category
feature_list : list of strings
contains names of all features that are used to generate
the feature value matrix (--> number of dimensions in the
model).
...note: this list has to be sorted !
Returns :
N x M matrix of N control feature values per feature (M).
Rows = Feature number /type
Columns = Feature values
"""
if not 'x' in self.fieldnames():
raise RuntimeError("""make_reg_data expects to find
(x,y) locations in self.x and self.y. But self.x does not exist""")
on_image = (self.x >= 0) & (self.x <= self.image_size[1])
on_image = on_image & (self.y >= 0) & (self.y <= self.image_size[0])
assert on_image.all(), "All Fixations need to be on the image"
assert len(np.unique(self.filenumber) > 1), "Fixmat has to have more than one filenumber"
self.x = self.x.astype(int)
self.y = self.y.astype(int)
if feature_list == None:
feature_list = np.sort(self._categories._features)
all_act = np.zeros((len(feature_list), 1)) * np.nan
all_ctrls = all_act.copy()
for (cfm, imgs) in self.by_cat():
# make a list of all filenumbers in this category and then
# choose one random filenumber without replacement
imfiles = np.array(imgs.images()) # array makes a copy of the list
ctrl_imgs = imfiles.copy()
np.random.shuffle(ctrl_imgs)
while (imfiles == ctrl_imgs).any():
np.random.shuffle(ctrl_imgs)
for (imidx, img) in enumerate(imfiles):
xact = cfm.x[cfm.filenumber == img]
yact = cfm.y[cfm.filenumber == img]
if all_controls:
# take a sample the same length as the actuals out of every
# non-fixated point in the feature map
idx = np.ones(self.image_size)
idx[cfm.y[cfm.filenumber == img],
cfm.x[cfm.filenumber == img]] = 0
yctrl, xctrl = idx.nonzero()
idx = np.random.randint(0, len(yctrl), len(xact))
yctrl = yctrl[idx]
xctrl = xctrl[idx]
del idx
else:
xctrl = cfm.x[cfm.filenumber == ctrl_imgs[imidx]]
yctrl = cfm.y[cfm.filenumber == ctrl_imgs[imidx]]
# initialize arrays for this filenumber
actuals = np.zeros((1, len(xact))) * np.nan
controls = np.zeros((1, len(xctrl))) * np.nan
for feature in feature_list:
# get the feature map
fmap = imgs[img][feature]
actuals = np.vstack((actuals, fmap[yact, xact]))
controls = np.vstack((controls, fmap[yctrl, xctrl]))
all_act = np.hstack((all_act, actuals[1:, :]))
all_ctrls = np.hstack((all_ctrls, controls[1:, :]))
return (all_act[:, 1:], all_ctrls[:, 1:])
|
python
|
def make_reg_data(self, feature_list=None, all_controls=False):
"""
Generates two M x N matrices with M feature values at fixations for
N features. Controls are a random sample out of all non-fixated regions
of an image or fixations of the same subject group on a randomly chosen
image. Fixations are pooled over all subjects in the calling fixmat.
Parameters :
all_controls : bool
if True, all non-fixated points on a feature map are takes as
control values. If False, controls are fixations from the same
subjects but on one other randomly chosen image of the same
category
feature_list : list of strings
contains names of all features that are used to generate
the feature value matrix (--> number of dimensions in the
model).
...note: this list has to be sorted !
Returns :
N x M matrix of N control feature values per feature (M).
Rows = Feature number /type
Columns = Feature values
"""
if not 'x' in self.fieldnames():
raise RuntimeError("""make_reg_data expects to find
(x,y) locations in self.x and self.y. But self.x does not exist""")
on_image = (self.x >= 0) & (self.x <= self.image_size[1])
on_image = on_image & (self.y >= 0) & (self.y <= self.image_size[0])
assert on_image.all(), "All Fixations need to be on the image"
assert len(np.unique(self.filenumber) > 1), "Fixmat has to have more than one filenumber"
self.x = self.x.astype(int)
self.y = self.y.astype(int)
if feature_list == None:
feature_list = np.sort(self._categories._features)
all_act = np.zeros((len(feature_list), 1)) * np.nan
all_ctrls = all_act.copy()
for (cfm, imgs) in self.by_cat():
# make a list of all filenumbers in this category and then
# choose one random filenumber without replacement
imfiles = np.array(imgs.images()) # array makes a copy of the list
ctrl_imgs = imfiles.copy()
np.random.shuffle(ctrl_imgs)
while (imfiles == ctrl_imgs).any():
np.random.shuffle(ctrl_imgs)
for (imidx, img) in enumerate(imfiles):
xact = cfm.x[cfm.filenumber == img]
yact = cfm.y[cfm.filenumber == img]
if all_controls:
# take a sample the same length as the actuals out of every
# non-fixated point in the feature map
idx = np.ones(self.image_size)
idx[cfm.y[cfm.filenumber == img],
cfm.x[cfm.filenumber == img]] = 0
yctrl, xctrl = idx.nonzero()
idx = np.random.randint(0, len(yctrl), len(xact))
yctrl = yctrl[idx]
xctrl = xctrl[idx]
del idx
else:
xctrl = cfm.x[cfm.filenumber == ctrl_imgs[imidx]]
yctrl = cfm.y[cfm.filenumber == ctrl_imgs[imidx]]
# initialize arrays for this filenumber
actuals = np.zeros((1, len(xact))) * np.nan
controls = np.zeros((1, len(xctrl))) * np.nan
for feature in feature_list:
# get the feature map
fmap = imgs[img][feature]
actuals = np.vstack((actuals, fmap[yact, xact]))
controls = np.vstack((controls, fmap[yctrl, xctrl]))
all_act = np.hstack((all_act, actuals[1:, :]))
all_ctrls = np.hstack((all_ctrls, controls[1:, :]))
return (all_act[:, 1:], all_ctrls[:, 1:])
|
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Parameters :
all_controls : bool
if True, all non-fixated points on a feature map are takes as
control values. If False, controls are fixations from the same
subjects but on one other randomly chosen image of the same
category
feature_list : list of strings
contains names of all features that are used to generate
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N x M matrix of N control feature values per feature (M).
Rows = Feature number /type
Columns = Feature values
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/fixmat.py#L62-L138
|
nwilming/ocupy
|
ocupy/samples2fix.py
|
get_velocity
|
def get_velocity(samplemat, Hz, blinks=None):
'''
Compute velocity of eye-movements.
Samplemat must contain fields 'x' and 'y', specifying the x,y coordinates
of gaze location. The function assumes that the values in x,y are sampled
continously at a rate specified by 'Hz'.
'''
Hz = float(Hz)
distance = ((np.diff(samplemat.x) ** 2) +
(np.diff(samplemat.y) ** 2)) ** .5
distance = np.hstack(([distance[0]], distance))
if blinks is not None:
distance[blinks[1:]] = np.nan
win = np.ones((velocity_window_size)) / float(velocity_window_size)
velocity = np.convolve(distance, win, mode='same')
velocity = velocity / (velocity_window_size / Hz)
acceleration = np.diff(velocity) / (1. / Hz)
acceleration = abs(np.hstack(([acceleration[0]], acceleration)))
return velocity, acceleration
|
python
|
def get_velocity(samplemat, Hz, blinks=None):
'''
Compute velocity of eye-movements.
Samplemat must contain fields 'x' and 'y', specifying the x,y coordinates
of gaze location. The function assumes that the values in x,y are sampled
continously at a rate specified by 'Hz'.
'''
Hz = float(Hz)
distance = ((np.diff(samplemat.x) ** 2) +
(np.diff(samplemat.y) ** 2)) ** .5
distance = np.hstack(([distance[0]], distance))
if blinks is not None:
distance[blinks[1:]] = np.nan
win = np.ones((velocity_window_size)) / float(velocity_window_size)
velocity = np.convolve(distance, win, mode='same')
velocity = velocity / (velocity_window_size / Hz)
acceleration = np.diff(velocity) / (1. / Hz)
acceleration = abs(np.hstack(([acceleration[0]], acceleration)))
return velocity, acceleration
|
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Compute velocity of eye-movements.
Samplemat must contain fields 'x' and 'y', specifying the x,y coordinates
of gaze location. The function assumes that the values in x,y are sampled
continously at a rate specified by 'Hz'.
|
[
"Compute",
"velocity",
"of",
"eye",
"-",
"movements",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/samples2fix.py#L11-L30
|
nwilming/ocupy
|
ocupy/samples2fix.py
|
saccade_detection
|
def saccade_detection(samplemat, Hz=200, threshold=30,
acc_thresh=2000, min_duration=21, min_movement=.35,
ignore_blinks=False):
'''
Detect saccades in a stream of gaze location samples.
Coordinates in samplemat are assumed to be in degrees.
Saccades are detect by a velocity/acceleration threshold approach.
A saccade starts when a) the velocity is above threshold, b) the
acceleration is above acc_thresh at least once during the interval
defined by the velocity threshold, c) the saccade lasts at least min_duration
ms and d) the distance between saccade start and enpoint is at least
min_movement degrees.
'''
if ignore_blinks:
velocity, acceleration = get_velocity(samplemat, float(Hz), blinks=samplemat.blinks)
else:
velocity, acceleration = get_velocity(samplemat, float(Hz))
saccades = (velocity > threshold)
#print velocity[samplemat.blinks[1:]]
#print saccades[samplemat.blinks[1:]]
borders = np.where(np.diff(saccades.astype(int)))[0] + 1
if velocity[1] > threshold:
borders = np.hstack(([0], borders))
saccade = 0 * np.ones(samplemat.x.shape)
# Only count saccades when acceleration also surpasses threshold
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
if sum(acceleration[start:end] > acc_thresh) >= 1:
saccade[start:end] = 1
borders = np.where(np.diff(saccade.astype(int)))[0] + 1
if saccade[0] == 0:
borders = np.hstack(([0], borders))
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
if (1000*(end - start) / float(Hz)) < (min_duration):
saccade[start:end] = 1
# Delete saccade between fixations that are too close together.
dists_ok = False
while not dists_ok:
dists_ok = True
num_merges = 0
for i, (lfixstart, lfixend, start, end, nfixstart, nfixend) in enumerate(zip(
borders[0::2], borders[1::2],
borders[1::2], borders[2::2],
borders[2::2], borders[3::2])):
lastx = samplemat.x[lfixstart:lfixend].mean()
lasty = samplemat.y[lfixstart:lfixend].mean()
nextx = samplemat.x[nfixstart:nfixend].mean()
nexty = samplemat.y[nfixstart:nfixend].mean()
if (1000*(lfixend - lfixstart) / float(Hz)) < (min_duration):
saccade[lfixstart:lfixend] = 1
continue
distance = ((nextx - lastx) ** 2 + (nexty - lasty) ** 2) ** .5
if distance < min_movement:
num_merges += 1
dists_ok = False
saccade[start:end] = 0
borders = np.where(np.diff(saccade.astype(int)))[0] + 1
if saccade[0] == 0:
borders = np.hstack(([0], borders))
return saccade.astype(bool)
|
python
|
def saccade_detection(samplemat, Hz=200, threshold=30,
acc_thresh=2000, min_duration=21, min_movement=.35,
ignore_blinks=False):
'''
Detect saccades in a stream of gaze location samples.
Coordinates in samplemat are assumed to be in degrees.
Saccades are detect by a velocity/acceleration threshold approach.
A saccade starts when a) the velocity is above threshold, b) the
acceleration is above acc_thresh at least once during the interval
defined by the velocity threshold, c) the saccade lasts at least min_duration
ms and d) the distance between saccade start and enpoint is at least
min_movement degrees.
'''
if ignore_blinks:
velocity, acceleration = get_velocity(samplemat, float(Hz), blinks=samplemat.blinks)
else:
velocity, acceleration = get_velocity(samplemat, float(Hz))
saccades = (velocity > threshold)
#print velocity[samplemat.blinks[1:]]
#print saccades[samplemat.blinks[1:]]
borders = np.where(np.diff(saccades.astype(int)))[0] + 1
if velocity[1] > threshold:
borders = np.hstack(([0], borders))
saccade = 0 * np.ones(samplemat.x.shape)
# Only count saccades when acceleration also surpasses threshold
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
if sum(acceleration[start:end] > acc_thresh) >= 1:
saccade[start:end] = 1
borders = np.where(np.diff(saccade.astype(int)))[0] + 1
if saccade[0] == 0:
borders = np.hstack(([0], borders))
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
if (1000*(end - start) / float(Hz)) < (min_duration):
saccade[start:end] = 1
# Delete saccade between fixations that are too close together.
dists_ok = False
while not dists_ok:
dists_ok = True
num_merges = 0
for i, (lfixstart, lfixend, start, end, nfixstart, nfixend) in enumerate(zip(
borders[0::2], borders[1::2],
borders[1::2], borders[2::2],
borders[2::2], borders[3::2])):
lastx = samplemat.x[lfixstart:lfixend].mean()
lasty = samplemat.y[lfixstart:lfixend].mean()
nextx = samplemat.x[nfixstart:nfixend].mean()
nexty = samplemat.y[nfixstart:nfixend].mean()
if (1000*(lfixend - lfixstart) / float(Hz)) < (min_duration):
saccade[lfixstart:lfixend] = 1
continue
distance = ((nextx - lastx) ** 2 + (nexty - lasty) ** 2) ** .5
if distance < min_movement:
num_merges += 1
dists_ok = False
saccade[start:end] = 0
borders = np.where(np.diff(saccade.astype(int)))[0] + 1
if saccade[0] == 0:
borders = np.hstack(([0], borders))
return saccade.astype(bool)
|
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Detect saccades in a stream of gaze location samples.
Coordinates in samplemat are assumed to be in degrees.
Saccades are detect by a velocity/acceleration threshold approach.
A saccade starts when a) the velocity is above threshold, b) the
acceleration is above acc_thresh at least once during the interval
defined by the velocity threshold, c) the saccade lasts at least min_duration
ms and d) the distance between saccade start and enpoint is at least
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|
[
"Detect",
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"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/samples2fix.py#L33-L98
|
nwilming/ocupy
|
ocupy/samples2fix.py
|
fixation_detection
|
def fixation_detection(samplemat, saccades, Hz=200, samples2fix=None,
respect_trial_borders=False, sample_times=None):
'''
Detect Fixation from saccades.
Fixations are defined as intervals between saccades. This function
also calcuates start and end times (in ms) for each fixation.
Input:
samplemat: datamat
Contains the recorded samples and associated metadata.
saccades: ndarray
Logical vector that is True for samples that belong to a saccade.
Hz: Float
Number of samples per second.
samples2fix: Dict
There is usually metadata associated with the samples (e.g. the
trial number). This dictionary can be used to specify how the
metadata should be collapsed for one fixation. It contains
field names from samplemat as keys and functions as values that
return one value when they are called with all samples for one
fixation. In addition the function can raise an 'InvalidFixation'
exception to signal that the fixation should be discarded.
'''
if samples2fix is None:
samples2fix = {}
fixations = ~saccades
acc = AccumulatorFactory()
if not respect_trial_borders:
borders = np.where(np.diff(fixations.astype(int)))[0] + 1
else:
borders = np.where(
~(np.diff(fixations.astype(int)) == 0) |
~(np.diff(samplemat.trial.astype(int)) == 0))[0] + 1
fixations = 0 * saccades.copy()
if not saccades[0]:
borders = np.hstack(([0], borders))
#lasts,laste = borders[0], borders[1]
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
current = {}
for k in samplemat.fieldnames():
if k in list(samples2fix.keys()):
current[k] = samples2fix[k](samplemat, k, start, end)
else:
current[k] = np.mean(samplemat.field(k)[start:end])
current['start_sample'] = start
current['end_sample'] = end
fixations[start:end] = 1
# Calculate start and end time in ms
if sample_times is None:
current['start'] = 1000 * start / Hz
current['end'] = 1000 * end / Hz
else:
current['start'] = sample_times[start]
current['end'] = sample_times[end]
#lasts, laste = start,end
acc.update(current)
return acc.get_dm(params=samplemat.parameters()), fixations.astype(bool)
|
python
|
def fixation_detection(samplemat, saccades, Hz=200, samples2fix=None,
respect_trial_borders=False, sample_times=None):
'''
Detect Fixation from saccades.
Fixations are defined as intervals between saccades. This function
also calcuates start and end times (in ms) for each fixation.
Input:
samplemat: datamat
Contains the recorded samples and associated metadata.
saccades: ndarray
Logical vector that is True for samples that belong to a saccade.
Hz: Float
Number of samples per second.
samples2fix: Dict
There is usually metadata associated with the samples (e.g. the
trial number). This dictionary can be used to specify how the
metadata should be collapsed for one fixation. It contains
field names from samplemat as keys and functions as values that
return one value when they are called with all samples for one
fixation. In addition the function can raise an 'InvalidFixation'
exception to signal that the fixation should be discarded.
'''
if samples2fix is None:
samples2fix = {}
fixations = ~saccades
acc = AccumulatorFactory()
if not respect_trial_borders:
borders = np.where(np.diff(fixations.astype(int)))[0] + 1
else:
borders = np.where(
~(np.diff(fixations.astype(int)) == 0) |
~(np.diff(samplemat.trial.astype(int)) == 0))[0] + 1
fixations = 0 * saccades.copy()
if not saccades[0]:
borders = np.hstack(([0], borders))
#lasts,laste = borders[0], borders[1]
for i, (start, end) in enumerate(zip(borders[0::2], borders[1::2])):
current = {}
for k in samplemat.fieldnames():
if k in list(samples2fix.keys()):
current[k] = samples2fix[k](samplemat, k, start, end)
else:
current[k] = np.mean(samplemat.field(k)[start:end])
current['start_sample'] = start
current['end_sample'] = end
fixations[start:end] = 1
# Calculate start and end time in ms
if sample_times is None:
current['start'] = 1000 * start / Hz
current['end'] = 1000 * end / Hz
else:
current['start'] = sample_times[start]
current['end'] = sample_times[end]
#lasts, laste = start,end
acc.update(current)
return acc.get_dm(params=samplemat.parameters()), fixations.astype(bool)
|
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"=",
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"]",
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"=",
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"[",
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"#lasts, laste = start,end",
"acc",
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"update",
"(",
"current",
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"samplemat",
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"parameters",
"(",
")",
")",
",",
"fixations",
".",
"astype",
"(",
"bool",
")"
] |
Detect Fixation from saccades.
Fixations are defined as intervals between saccades. This function
also calcuates start and end times (in ms) for each fixation.
Input:
samplemat: datamat
Contains the recorded samples and associated metadata.
saccades: ndarray
Logical vector that is True for samples that belong to a saccade.
Hz: Float
Number of samples per second.
samples2fix: Dict
There is usually metadata associated with the samples (e.g. the
trial number). This dictionary can be used to specify how the
metadata should be collapsed for one fixation. It contains
field names from samplemat as keys and functions as values that
return one value when they are called with all samples for one
fixation. In addition the function can raise an 'InvalidFixation'
exception to signal that the fixation should be discarded.
|
[
"Detect",
"Fixation",
"from",
"saccades",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/samples2fix.py#L101-L161
|
kurtmckee/listparser
|
listparser/__init__.py
|
parse
|
def parse(parse_obj, agent=None, etag=None, modified=None, inject=False):
"""Parse a subscription list and return a dict containing the results.
:param parse_obj: A file-like object or a string containing a URL, an
absolute or relative filename, or an XML document.
:type parse_obj: str or file
:param agent: User-Agent header to be sent when requesting a URL
:type agent: str
:param etag: The ETag header to be sent when requesting a URL.
:type etag: str
:param modified: The Last-Modified header to be sent when requesting a URL.
:type modified: str or datetime.datetime
:returns: All of the parsed information, webserver HTTP response
headers, and any exception encountered.
:rtype: dict
:py:func:`~listparser.parse` is the only public function exposed by
listparser.
If *parse_obj* is a URL, the *agent* will identify the software
making the request, *etag* will identify the last HTTP ETag
header returned by the webserver, and *modified* will
identify the last HTTP Last-Modified header returned by the
webserver. *agent* and *etag* must be strings,
while *modified* can be either a string or a Python
*datetime.datetime* object.
If *agent* is not provided, the :py:data:`~listparser.USER_AGENT` global
variable will be used by default.
"""
guarantees = common.SuperDict({
'bozo': 0,
'feeds': [],
'lists': [],
'opportunities': [],
'meta': common.SuperDict(),
'version': '',
})
fileobj, info = _mkfile(parse_obj, (agent or USER_AGENT), etag, modified)
guarantees.update(info)
if not fileobj:
return guarantees
handler = Handler()
handler.harvest.update(guarantees)
parser = xml.sax.make_parser()
parser.setFeature(xml.sax.handler.feature_namespaces, True)
parser.setContentHandler(handler)
parser.setErrorHandler(handler)
if inject:
fileobj = Injector(fileobj)
try:
parser.parse(fileobj)
except (SAXParseException, MalformedByteSequenceException): # noqa: E501 # pragma: no cover
# Jython propagates exceptions past the ErrorHandler.
err = sys.exc_info()[1]
handler.harvest.bozo = 1
handler.harvest.bozo_exception = err
finally:
fileobj.close()
# Test if a DOCTYPE injection is needed
if hasattr(handler.harvest, 'bozo_exception'):
if 'entity' in handler.harvest.bozo_exception.__str__():
if not inject:
return parse(parse_obj, agent, etag, modified, True)
# Make it clear that the XML file is broken
# (if no other exception has been assigned)
if inject and not handler.harvest.bozo:
handler.harvest.bozo = 1
handler.harvest.bozo_exception = ListError('undefined entity found')
return handler.harvest
|
python
|
def parse(parse_obj, agent=None, etag=None, modified=None, inject=False):
"""Parse a subscription list and return a dict containing the results.
:param parse_obj: A file-like object or a string containing a URL, an
absolute or relative filename, or an XML document.
:type parse_obj: str or file
:param agent: User-Agent header to be sent when requesting a URL
:type agent: str
:param etag: The ETag header to be sent when requesting a URL.
:type etag: str
:param modified: The Last-Modified header to be sent when requesting a URL.
:type modified: str or datetime.datetime
:returns: All of the parsed information, webserver HTTP response
headers, and any exception encountered.
:rtype: dict
:py:func:`~listparser.parse` is the only public function exposed by
listparser.
If *parse_obj* is a URL, the *agent* will identify the software
making the request, *etag* will identify the last HTTP ETag
header returned by the webserver, and *modified* will
identify the last HTTP Last-Modified header returned by the
webserver. *agent* and *etag* must be strings,
while *modified* can be either a string or a Python
*datetime.datetime* object.
If *agent* is not provided, the :py:data:`~listparser.USER_AGENT` global
variable will be used by default.
"""
guarantees = common.SuperDict({
'bozo': 0,
'feeds': [],
'lists': [],
'opportunities': [],
'meta': common.SuperDict(),
'version': '',
})
fileobj, info = _mkfile(parse_obj, (agent or USER_AGENT), etag, modified)
guarantees.update(info)
if not fileobj:
return guarantees
handler = Handler()
handler.harvest.update(guarantees)
parser = xml.sax.make_parser()
parser.setFeature(xml.sax.handler.feature_namespaces, True)
parser.setContentHandler(handler)
parser.setErrorHandler(handler)
if inject:
fileobj = Injector(fileobj)
try:
parser.parse(fileobj)
except (SAXParseException, MalformedByteSequenceException): # noqa: E501 # pragma: no cover
# Jython propagates exceptions past the ErrorHandler.
err = sys.exc_info()[1]
handler.harvest.bozo = 1
handler.harvest.bozo_exception = err
finally:
fileobj.close()
# Test if a DOCTYPE injection is needed
if hasattr(handler.harvest, 'bozo_exception'):
if 'entity' in handler.harvest.bozo_exception.__str__():
if not inject:
return parse(parse_obj, agent, etag, modified, True)
# Make it clear that the XML file is broken
# (if no other exception has been assigned)
if inject and not handler.harvest.bozo:
handler.harvest.bozo = 1
handler.harvest.bozo_exception = ListError('undefined entity found')
return handler.harvest
|
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Parse a subscription list and return a dict containing the results.
:param parse_obj: A file-like object or a string containing a URL, an
absolute or relative filename, or an XML document.
:type parse_obj: str or file
:param agent: User-Agent header to be sent when requesting a URL
:type agent: str
:param etag: The ETag header to be sent when requesting a URL.
:type etag: str
:param modified: The Last-Modified header to be sent when requesting a URL.
:type modified: str or datetime.datetime
:returns: All of the parsed information, webserver HTTP response
headers, and any exception encountered.
:rtype: dict
:py:func:`~listparser.parse` is the only public function exposed by
listparser.
If *parse_obj* is a URL, the *agent* will identify the software
making the request, *etag* will identify the last HTTP ETag
header returned by the webserver, and *modified* will
identify the last HTTP Last-Modified header returned by the
webserver. *agent* and *etag* must be strings,
while *modified* can be either a string or a Python
*datetime.datetime* object.
If *agent* is not provided, the :py:data:`~listparser.USER_AGENT` global
variable will be used by default.
|
[
"Parse",
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"list",
"and",
"return",
"a",
"dict",
"containing",
"the",
"results",
"."
] |
train
|
https://github.com/kurtmckee/listparser/blob/f9bc310a0ce567cd0611fea68be99974021f53c7/listparser/__init__.py#L71-L144
|
nwilming/ocupy
|
ocupy/stimuli.py
|
FixmatStimuliFactory
|
def FixmatStimuliFactory(fm, loader):
"""
Constructs an categories object for all image / category
combinations in the fixmat.
Parameters:
fm: FixMat
Used for extracting valid category/image combination.
loader: loader
Loader that accesses the stimuli for this fixmat
Returns:
Categories object
"""
# Find all feature names
features = []
if loader.ftrpath:
assert os.access(loader.ftrpath, os.R_OK)
features = os.listdir(os.path.join(loader.ftrpath, str(fm.category[0])))
# Find all images in all categories
img_per_cat = {}
for cat in np.unique(fm.category):
if not loader.test_for_category(cat):
raise ValueError('Category %s is specified in fixmat but '%(
str(cat) + 'can not be located by loader'))
img_per_cat[cat] = []
for img in np.unique(fm[(fm.category == cat)].filenumber):
if not loader.test_for_image(cat, img):
raise ValueError('Image %s in category %s is '%(str(cat),
str(img)) +
'specified in fixmat but can be located by loader')
img_per_cat[cat].append(img)
if loader.ftrpath:
for feature in features:
if not loader.test_for_feature(cat, img, feature):
raise RuntimeError(
'Feature %s for image %s' %(str(feature),str(img)) +
' in category %s ' %str(cat) +
'can not be located by loader')
return Categories(loader, img_per_cat = img_per_cat,
features = features, fixations = fm)
|
python
|
def FixmatStimuliFactory(fm, loader):
"""
Constructs an categories object for all image / category
combinations in the fixmat.
Parameters:
fm: FixMat
Used for extracting valid category/image combination.
loader: loader
Loader that accesses the stimuli for this fixmat
Returns:
Categories object
"""
# Find all feature names
features = []
if loader.ftrpath:
assert os.access(loader.ftrpath, os.R_OK)
features = os.listdir(os.path.join(loader.ftrpath, str(fm.category[0])))
# Find all images in all categories
img_per_cat = {}
for cat in np.unique(fm.category):
if not loader.test_for_category(cat):
raise ValueError('Category %s is specified in fixmat but '%(
str(cat) + 'can not be located by loader'))
img_per_cat[cat] = []
for img in np.unique(fm[(fm.category == cat)].filenumber):
if not loader.test_for_image(cat, img):
raise ValueError('Image %s in category %s is '%(str(cat),
str(img)) +
'specified in fixmat but can be located by loader')
img_per_cat[cat].append(img)
if loader.ftrpath:
for feature in features:
if not loader.test_for_feature(cat, img, feature):
raise RuntimeError(
'Feature %s for image %s' %(str(feature),str(img)) +
' in category %s ' %str(cat) +
'can not be located by loader')
return Categories(loader, img_per_cat = img_per_cat,
features = features, fixations = fm)
|
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Constructs an categories object for all image / category
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Parameters:
fm: FixMat
Used for extracting valid category/image combination.
loader: loader
Loader that accesses the stimuli for this fixmat
Returns:
Categories object
|
[
"Constructs",
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/stimuli.py#L177-L217
|
nwilming/ocupy
|
ocupy/stimuli.py
|
DirectoryStimuliFactory
|
def DirectoryStimuliFactory(loader):
"""
Takes an input path to the images folder of an experiment and generates
automatically the category - filenumber list needed to construct an
appropriate _categories object.
Parameters :
loader : Loader object which contains
impath : string
path to the input, i.e. image-, files of the experiment. All
subfolders in that path will be treated as categories. If no
subfolders are present, category 1 will be assigned and all
files in the folder are considered input images.
Images have to end in '.png'.
ftrpath : string
path to the feature folder. It is expected that the folder
structure corresponds to the structure in impath, i.e.
ftrpath/category/featurefolder/featuremap.mat
Furthermore, features are assumed to be the same for all
categories.
"""
impath = loader.impath
ftrpath = loader.ftrpath
# checks whether user has reading permission for the path
assert os.access(impath, os.R_OK)
assert os.access(ftrpath, os.R_OK)
# EXTRACTING IMAGE NAMES
img_per_cat = {}
# extract only directories in the given folder
subfolders = [name for name in os.listdir(impath) if os.path.isdir(
os.path.join(impath, name))]
# if there are no subfolders, walk through files. Take 1 as key for the
# categories object
if not subfolders:
[_, _, files] = next(os.walk(os.path.join(impath)))
# this only takes entries that end with '.png'
entries = {1:
[int(cur_file[cur_file.find('_')+1:-4]) for cur_file
in files if cur_file.endswith('.png')]}
img_per_cat.update(entries)
subfolders = ['']
# if there are subfolders, walk through them
else:
for directory in subfolders:
[_, _, files] = next(os.walk(os.path.join(impath, directory)))
# this only takes entries that end with '.png'. Strips ending and
# considers everything after the first '_' as the imagenumber
imagenumbers = [int(cur_file[cur_file.find('_')+1:-4])
for cur_file in files
if (cur_file.endswith('.png') & (len(cur_file) > 4))]
entries = {int(directory): imagenumbers}
img_per_cat.update(entries)
del directory
del imagenumbers
# in case subfolders do not exist, '' is appended here.
_, features, files = next(os.walk(os.path.join(ftrpath,
subfolders[0])))
return Categories(loader, img_per_cat = img_per_cat, features = features)
|
python
|
def DirectoryStimuliFactory(loader):
"""
Takes an input path to the images folder of an experiment and generates
automatically the category - filenumber list needed to construct an
appropriate _categories object.
Parameters :
loader : Loader object which contains
impath : string
path to the input, i.e. image-, files of the experiment. All
subfolders in that path will be treated as categories. If no
subfolders are present, category 1 will be assigned and all
files in the folder are considered input images.
Images have to end in '.png'.
ftrpath : string
path to the feature folder. It is expected that the folder
structure corresponds to the structure in impath, i.e.
ftrpath/category/featurefolder/featuremap.mat
Furthermore, features are assumed to be the same for all
categories.
"""
impath = loader.impath
ftrpath = loader.ftrpath
# checks whether user has reading permission for the path
assert os.access(impath, os.R_OK)
assert os.access(ftrpath, os.R_OK)
# EXTRACTING IMAGE NAMES
img_per_cat = {}
# extract only directories in the given folder
subfolders = [name for name in os.listdir(impath) if os.path.isdir(
os.path.join(impath, name))]
# if there are no subfolders, walk through files. Take 1 as key for the
# categories object
if not subfolders:
[_, _, files] = next(os.walk(os.path.join(impath)))
# this only takes entries that end with '.png'
entries = {1:
[int(cur_file[cur_file.find('_')+1:-4]) for cur_file
in files if cur_file.endswith('.png')]}
img_per_cat.update(entries)
subfolders = ['']
# if there are subfolders, walk through them
else:
for directory in subfolders:
[_, _, files] = next(os.walk(os.path.join(impath, directory)))
# this only takes entries that end with '.png'. Strips ending and
# considers everything after the first '_' as the imagenumber
imagenumbers = [int(cur_file[cur_file.find('_')+1:-4])
for cur_file in files
if (cur_file.endswith('.png') & (len(cur_file) > 4))]
entries = {int(directory): imagenumbers}
img_per_cat.update(entries)
del directory
del imagenumbers
# in case subfolders do not exist, '' is appended here.
_, features, files = next(os.walk(os.path.join(ftrpath,
subfolders[0])))
return Categories(loader, img_per_cat = img_per_cat, features = features)
|
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Parameters :
loader : Loader object which contains
impath : string
path to the input, i.e. image-, files of the experiment. All
subfolders in that path will be treated as categories. If no
subfolders are present, category 1 will be assigned and all
files in the folder are considered input images.
Images have to end in '.png'.
ftrpath : string
path to the feature folder. It is expected that the folder
structure corresponds to the structure in impath, i.e.
ftrpath/category/featurefolder/featuremap.mat
Furthermore, features are assumed to be the same for all
categories.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/stimuli.py#L219-L278
|
nwilming/ocupy
|
ocupy/stimuli.py
|
Categories.fixations
|
def fixations(self):
''' Filter the fixmat such that it only contains fixations on images
in categories that are also in the categories object'''
if not self._fixations:
raise RuntimeError('This Images object does not have'
+' an associated fixmat')
if len(list(self._categories.keys())) == 0:
return None
else:
idx = np.zeros(self._fixations.x.shape, dtype='bool')
for (cat, _) in list(self._categories.items()):
idx = idx | ((self._fixations.category == cat))
return self._fixations[idx]
|
python
|
def fixations(self):
''' Filter the fixmat such that it only contains fixations on images
in categories that are also in the categories object'''
if not self._fixations:
raise RuntimeError('This Images object does not have'
+' an associated fixmat')
if len(list(self._categories.keys())) == 0:
return None
else:
idx = np.zeros(self._fixations.x.shape, dtype='bool')
for (cat, _) in list(self._categories.items()):
idx = idx | ((self._fixations.category == cat))
return self._fixations[idx]
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/stimuli.py#L49-L61
|
nwilming/ocupy
|
ocupy/stimuli.py
|
Image.data
|
def data(self, value):
"""
Saves a new image to disk
"""
self.loader.save_image(self.category, self.image, value)
|
python
|
def data(self, value):
"""
Saves a new image to disk
"""
self.loader.save_image(self.category, self.image, value)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/stimuli.py#L140-L144
|
nwilming/ocupy
|
ocupy/stimuli.py
|
Image.fixations
|
def fixations(self):
"""
Returns all fixations that are on this image.
A precondition for this to work is that a fixmat
is associated with this Image object.
"""
if not self._fixations:
raise RuntimeError('This Images object does not have'
+' an associated fixmat')
return self._fixations[(self._fixations.category == self.category) &
(self._fixations.filenumber == self.image)]
|
python
|
def fixations(self):
"""
Returns all fixations that are on this image.
A precondition for this to work is that a fixmat
is associated with this Image object.
"""
if not self._fixations:
raise RuntimeError('This Images object does not have'
+' an associated fixmat')
return self._fixations[(self._fixations.category == self.category) &
(self._fixations.filenumber == self.image)]
|
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Returns all fixations that are on this image.
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/stimuli.py#L164-L174
|
nwilming/ocupy
|
ocupy/xvalidation.py
|
SimpleXValidation.generate
|
def generate(self):
"""
Generator for creating the cross-validation slices.
Returns
A tuple of that contains two fixmats (training and test)
and two Category objects (test and train).
"""
for _ in range(0, self.num_slices):
#1. separate fixmat into test and training fixmat
subjects = np.unique(self.fm.SUBJECTINDEX)
test_subs = randsample(subjects,
self.subject_hold_out*len(subjects))
train_subs = [x for x in subjects if x not in test_subs]
test_fm = self.fm[ismember(self.fm.SUBJECTINDEX, test_subs)]
train_fm = self.fm[ismember(self.fm.SUBJECTINDEX, train_subs)]
#2. distribute images
test_imgs = {}
train_imgs = {}
id_test = (test_fm.x <1) & False
id_train = (train_fm.x <1) & False
for cat in self.categories:
imgs = cat.images()
test_imgs.update({cat.category:randsample(imgs,
self.image_hold_out*len(imgs)).tolist()})
train_imgs.update({cat.category:[x for x in imgs
if not ismember(x, test_imgs[cat.category])]})
id_test = id_test | ((ismember(test_fm.filenumber,
test_imgs[cat.category])) &
(test_fm.category == cat.category))
id_train = id_train | ((ismember(train_fm.filenumber,
train_imgs[cat.category])) &
(train_fm.category == cat.category))
#3. Create categories objects and yield result
test_stimuli = Categories(self.categories.loader, test_imgs,
features=self.categories._features,
fixations=test_fm)
train_stimuli = Categories(self.categories.loader, train_imgs,
features=self.categories._features,
fixations=train_fm)
yield (train_fm[id_train],
train_stimuli,
test_fm[id_test],
test_stimuli)
|
python
|
def generate(self):
"""
Generator for creating the cross-validation slices.
Returns
A tuple of that contains two fixmats (training and test)
and two Category objects (test and train).
"""
for _ in range(0, self.num_slices):
#1. separate fixmat into test and training fixmat
subjects = np.unique(self.fm.SUBJECTINDEX)
test_subs = randsample(subjects,
self.subject_hold_out*len(subjects))
train_subs = [x for x in subjects if x not in test_subs]
test_fm = self.fm[ismember(self.fm.SUBJECTINDEX, test_subs)]
train_fm = self.fm[ismember(self.fm.SUBJECTINDEX, train_subs)]
#2. distribute images
test_imgs = {}
train_imgs = {}
id_test = (test_fm.x <1) & False
id_train = (train_fm.x <1) & False
for cat in self.categories:
imgs = cat.images()
test_imgs.update({cat.category:randsample(imgs,
self.image_hold_out*len(imgs)).tolist()})
train_imgs.update({cat.category:[x for x in imgs
if not ismember(x, test_imgs[cat.category])]})
id_test = id_test | ((ismember(test_fm.filenumber,
test_imgs[cat.category])) &
(test_fm.category == cat.category))
id_train = id_train | ((ismember(train_fm.filenumber,
train_imgs[cat.category])) &
(train_fm.category == cat.category))
#3. Create categories objects and yield result
test_stimuli = Categories(self.categories.loader, test_imgs,
features=self.categories._features,
fixations=test_fm)
train_stimuli = Categories(self.categories.loader, train_imgs,
features=self.categories._features,
fixations=train_fm)
yield (train_fm[id_train],
train_stimuli,
test_fm[id_test],
test_stimuli)
|
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|
[
"Generator",
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"-",
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/xvalidation.py#L42-L88
|
nwilming/ocupy
|
ocupy/saccade_geometry.py
|
prepare_data
|
def prepare_data(fm, max_back, dur_cap=700):
'''
Computes angle and length differences up to given order and deletes
suspiciously long fixations.
Input
fm: Fixmat
Fixmat for which to comput angle and length differences
max_back: Int
Computes delta angle and amplitude up to order max_back.
dur_cap: Int
Longest allowed fixation duration
Output
fm: Fixmat
Filtered fixmat that aligns to the other outputs.
durations: ndarray
Duration for each fixation in fm
forward_angle:
Angle between previous and next saccade.
'''
durations = np.roll(fm.end - fm.start, 1).astype(float)
angles, lengths, ads, lds = anglendiff(fm, roll=max_back, return_abs=True)
# durations and ads are aligned in a way that an entry in ads
# encodes the angle of the saccade away from a fixation in
# durations
forward_angle = abs(reshift(ads[0])).astype(float)
ads = [abs(reshift(a)) for a in ads]
# Now filter out weird fixation durations
id_in = durations > dur_cap
durations[id_in] = np.nan
forward_angle[id_in] = np.nan
return fm, durations, forward_angle, ads, lds
|
python
|
def prepare_data(fm, max_back, dur_cap=700):
'''
Computes angle and length differences up to given order and deletes
suspiciously long fixations.
Input
fm: Fixmat
Fixmat for which to comput angle and length differences
max_back: Int
Computes delta angle and amplitude up to order max_back.
dur_cap: Int
Longest allowed fixation duration
Output
fm: Fixmat
Filtered fixmat that aligns to the other outputs.
durations: ndarray
Duration for each fixation in fm
forward_angle:
Angle between previous and next saccade.
'''
durations = np.roll(fm.end - fm.start, 1).astype(float)
angles, lengths, ads, lds = anglendiff(fm, roll=max_back, return_abs=True)
# durations and ads are aligned in a way that an entry in ads
# encodes the angle of the saccade away from a fixation in
# durations
forward_angle = abs(reshift(ads[0])).astype(float)
ads = [abs(reshift(a)) for a in ads]
# Now filter out weird fixation durations
id_in = durations > dur_cap
durations[id_in] = np.nan
forward_angle[id_in] = np.nan
return fm, durations, forward_angle, ads, lds
|
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Computes angle and length differences up to given order and deletes
suspiciously long fixations.
Input
fm: Fixmat
Fixmat for which to comput angle and length differences
max_back: Int
Computes delta angle and amplitude up to order max_back.
dur_cap: Int
Longest allowed fixation duration
Output
fm: Fixmat
Filtered fixmat that aligns to the other outputs.
durations: ndarray
Duration for each fixation in fm
forward_angle:
Angle between previous and next saccade.
|
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/saccade_geometry.py#L15-L48
|
nwilming/ocupy
|
ocupy/saccade_geometry.py
|
saccadic_momentum_effect
|
def saccadic_momentum_effect(durations, forward_angle,
summary_stat=nanmean):
"""
Computes the mean fixation duration at forward angles.
"""
durations_per_da = np.nan * np.ones((len(e_angle) - 1,))
for i, (bo, b1) in enumerate(zip(e_angle[:-1], e_angle[1:])):
idx = (
bo <= forward_angle) & (
forward_angle < b1) & (
~np.isnan(durations))
durations_per_da[i] = summary_stat(durations[idx])
return durations_per_da
|
python
|
def saccadic_momentum_effect(durations, forward_angle,
summary_stat=nanmean):
"""
Computes the mean fixation duration at forward angles.
"""
durations_per_da = np.nan * np.ones((len(e_angle) - 1,))
for i, (bo, b1) in enumerate(zip(e_angle[:-1], e_angle[1:])):
idx = (
bo <= forward_angle) & (
forward_angle < b1) & (
~np.isnan(durations))
durations_per_da[i] = summary_stat(durations[idx])
return durations_per_da
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/saccade_geometry.py#L51-L63
|
nwilming/ocupy
|
ocupy/saccade_geometry.py
|
ior_effect
|
def ior_effect(durations, angle_diffs, length_diffs,
summary_stat=np.mean, parallel=True, min_samples=20):
"""
Computes a measure of fixation durations at delta angle and delta
length combinations.
"""
raster = np.empty((len(e_dist) - 1, len(e_angle) - 1), dtype=object)
for a, (a_low, a_upp) in enumerate(zip(e_angle[:-1], e_angle[1:])):
for d, (d_low, d_upp) in enumerate(zip(e_dist[:-1], e_dist[1:])):
idx = ((d_low <= length_diffs) & (length_diffs < d_upp) &
(a_low <= angle_diffs) & (angle_diffs < a_upp))
if sum(idx) < min_samples:
raster[d, a] = np.array([np.nan])
else:
raster[d, a] = durations[idx]
if parallel:
p = pool.Pool(3)
result = p.map(summary_stat, list(raster.flatten()))
p.terminate()
else:
result = list(map(summary_stat, list(raster.flatten())))
for idx, value in enumerate(result):
i, j = np.unravel_index(idx, raster.shape)
raster[i, j] = value
return raster
|
python
|
def ior_effect(durations, angle_diffs, length_diffs,
summary_stat=np.mean, parallel=True, min_samples=20):
"""
Computes a measure of fixation durations at delta angle and delta
length combinations.
"""
raster = np.empty((len(e_dist) - 1, len(e_angle) - 1), dtype=object)
for a, (a_low, a_upp) in enumerate(zip(e_angle[:-1], e_angle[1:])):
for d, (d_low, d_upp) in enumerate(zip(e_dist[:-1], e_dist[1:])):
idx = ((d_low <= length_diffs) & (length_diffs < d_upp) &
(a_low <= angle_diffs) & (angle_diffs < a_upp))
if sum(idx) < min_samples:
raster[d, a] = np.array([np.nan])
else:
raster[d, a] = durations[idx]
if parallel:
p = pool.Pool(3)
result = p.map(summary_stat, list(raster.flatten()))
p.terminate()
else:
result = list(map(summary_stat, list(raster.flatten())))
for idx, value in enumerate(result):
i, j = np.unravel_index(idx, raster.shape)
raster[i, j] = value
return raster
|
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/saccade_geometry.py#L66-L90
|
nwilming/ocupy
|
ocupy/saccade_geometry.py
|
predict_fixation_duration
|
def predict_fixation_duration(
durations, angles, length_diffs, dataset=None, params=None):
"""
Fits a non-linear piecewise regression to fixtaion durations for a fixmat.
Returns corrected fixation durations.
"""
if dataset is None:
dataset = np.ones(durations.shape)
corrected_durations = np.nan * np.ones(durations.shape)
for i, ds in enumerate(np.unique(dataset)):
e = lambda v, x, y, z: (leastsq_dual_model(x, z, *v) - y)
v0 = [120, 220.0, -.1, 0.5, .1, .1]
id_ds = dataset == ds
idnan = (
~np.isnan(angles)) & (
~np.isnan(durations)) & (
~np.isnan(length_diffs))
v, s = leastsq(
e, v0, args=(
angles[
idnan & id_ds], durations[
idnan & id_ds], length_diffs[
idnan & id_ds]), maxfev=10000)
corrected_durations[id_ds] = (durations[id_ds] -
(leastsq_dual_model(angles[id_ds], length_diffs[id_ds], *v)))
if params is not None:
params['v' + str(i)] = v
params['s' + str(i)] = s
return corrected_durations
|
python
|
def predict_fixation_duration(
durations, angles, length_diffs, dataset=None, params=None):
"""
Fits a non-linear piecewise regression to fixtaion durations for a fixmat.
Returns corrected fixation durations.
"""
if dataset is None:
dataset = np.ones(durations.shape)
corrected_durations = np.nan * np.ones(durations.shape)
for i, ds in enumerate(np.unique(dataset)):
e = lambda v, x, y, z: (leastsq_dual_model(x, z, *v) - y)
v0 = [120, 220.0, -.1, 0.5, .1, .1]
id_ds = dataset == ds
idnan = (
~np.isnan(angles)) & (
~np.isnan(durations)) & (
~np.isnan(length_diffs))
v, s = leastsq(
e, v0, args=(
angles[
idnan & id_ds], durations[
idnan & id_ds], length_diffs[
idnan & id_ds]), maxfev=10000)
corrected_durations[id_ds] = (durations[id_ds] -
(leastsq_dual_model(angles[id_ds], length_diffs[id_ds], *v)))
if params is not None:
params['v' + str(i)] = v
params['s' + str(i)] = s
return corrected_durations
|
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/saccade_geometry.py#L93-L122
|
nwilming/ocupy
|
ocupy/saccade_geometry.py
|
subject_predictions
|
def subject_predictions(fm, field='SUBJECTINDEX',
method=predict_fixation_duration, data=None):
'''
Calculates the saccadic momentum effect for individual subjects.
Removes any effect of amplitude differences.
The parameters are fitted on unbinned data. The effects are
computed on binned data. See e_dist and e_angle for the binning
parameter.
'''
if data is None:
fma, dura, faa, adsa, ldsa = prepare_data(fm, dur_cap=700, max_back=5)
adsa = adsa[0]
ldsa = ldsa[0]
else:
fma, dura, faa, adsa, ldsa = data
fma = fma.copy() # [ones(fm.x.shape)]
sub_effects = []
sub_predictions = []
parameters = []
for i, fmsub in enumerate(np.unique(fma.field(field))):
id = fma.field(field) == fmsub
#_, dur, fa, ads, lds = prepare_data(fmsub, dur_cap = 700, max_back=5)
dur, fa, ads, lds = dura[id], faa[id], adsa[id], ldsa[id]
params = {}
_ = method(dur, fa, lds, params=params)
ps = params['v0']
ld_corrected = leastsq_only_dist(lds, ps[4], ps[5])
prediction = leastsq_only_angle(fa, ps[0], ps[1], ps[2], ps[3])
sub_predictions += [saccadic_momentum_effect(prediction, fa)]
sub_effects += [saccadic_momentum_effect(dur - ld_corrected, fa)]
parameters += [ps]
return np.array(sub_effects), np.array(sub_predictions), parameters
|
python
|
def subject_predictions(fm, field='SUBJECTINDEX',
method=predict_fixation_duration, data=None):
'''
Calculates the saccadic momentum effect for individual subjects.
Removes any effect of amplitude differences.
The parameters are fitted on unbinned data. The effects are
computed on binned data. See e_dist and e_angle for the binning
parameter.
'''
if data is None:
fma, dura, faa, adsa, ldsa = prepare_data(fm, dur_cap=700, max_back=5)
adsa = adsa[0]
ldsa = ldsa[0]
else:
fma, dura, faa, adsa, ldsa = data
fma = fma.copy() # [ones(fm.x.shape)]
sub_effects = []
sub_predictions = []
parameters = []
for i, fmsub in enumerate(np.unique(fma.field(field))):
id = fma.field(field) == fmsub
#_, dur, fa, ads, lds = prepare_data(fmsub, dur_cap = 700, max_back=5)
dur, fa, ads, lds = dura[id], faa[id], adsa[id], ldsa[id]
params = {}
_ = method(dur, fa, lds, params=params)
ps = params['v0']
ld_corrected = leastsq_only_dist(lds, ps[4], ps[5])
prediction = leastsq_only_angle(fa, ps[0], ps[1], ps[2], ps[3])
sub_predictions += [saccadic_momentum_effect(prediction, fa)]
sub_effects += [saccadic_momentum_effect(dur - ld_corrected, fa)]
parameters += [ps]
return np.array(sub_effects), np.array(sub_predictions), parameters
|
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Calculates the saccadic momentum effect for individual subjects.
Removes any effect of amplitude differences.
The parameters are fitted on unbinned data. The effects are
computed on binned data. See e_dist and e_angle for the binning
parameter.
|
[
"Calculates",
"the",
"saccadic",
"momentum",
"effect",
"for",
"individual",
"subjects",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/saccade_geometry.py#L125-L158
|
nwilming/ocupy
|
ocupy/bounds.py
|
intersubject_scores
|
def intersubject_scores(fm, category, predicting_filenumbers,
predicting_subjects, predicted_filenumbers,
predicted_subjects, controls = True, scale_factor = 1):
"""
Calculates how well the fixations from a set of subjects on a set of
images can be predicted with the fixations from another set of subjects
on another set of images.
The prediction is carried out by computing a fixation density map from
fixations of predicting_subjects subjects on predicting_images images.
Prediction accuracy is assessed by measures.prediction_scores.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
predicting_filenumbers : list
List of filenumbers used for prediction, i.e. images where fixations
for the prediction are taken from.
predicting_subjects : list
List of subjects whose fixations on images in predicting_filenumbers
are used for the prediction.
predicted_filenumnbers : list
List of images from which the to be predicted fixations are taken.
predicted_subjects : list
List of subjects used for evaluation, i.e subjects whose fixations
on images in predicted_filenumbers are taken for evaluation.
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
auc : area under the roc curve for sets of actuals and controls
true_pos_rate : ndarray
Rate of true positives for every given threshold value.
All values appearing in actuals are taken as thresholds. Uses lower
sum interpolation.
false_pos_rate : ndarray
See true_pos_rate but for false positives.
"""
predicting_fm = fm[
(ismember(fm.SUBJECTINDEX, predicting_subjects)) &
(ismember(fm.filenumber, predicting_filenumbers)) &
(fm.category == category)]
predicted_fm = fm[
(ismember(fm.SUBJECTINDEX,predicted_subjects)) &
(ismember(fm.filenumber,predicted_filenumbers))&
(fm.category == category)]
try:
predicting_fdm = compute_fdm(predicting_fm, scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
if controls == True:
fm_controls = fm[
(ismember(fm.SUBJECTINDEX, predicted_subjects)) &
((ismember(fm.filenumber, predicted_filenumbers)) != True) &
(fm.category == category)]
return measures.prediction_scores(predicting_fdm, predicted_fm,
controls = (fm_controls.y, fm_controls.x))
return measures.prediction_scores(predicting_fdm, predicted_fm, controls = None)
|
python
|
def intersubject_scores(fm, category, predicting_filenumbers,
predicting_subjects, predicted_filenumbers,
predicted_subjects, controls = True, scale_factor = 1):
"""
Calculates how well the fixations from a set of subjects on a set of
images can be predicted with the fixations from another set of subjects
on another set of images.
The prediction is carried out by computing a fixation density map from
fixations of predicting_subjects subjects on predicting_images images.
Prediction accuracy is assessed by measures.prediction_scores.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
predicting_filenumbers : list
List of filenumbers used for prediction, i.e. images where fixations
for the prediction are taken from.
predicting_subjects : list
List of subjects whose fixations on images in predicting_filenumbers
are used for the prediction.
predicted_filenumnbers : list
List of images from which the to be predicted fixations are taken.
predicted_subjects : list
List of subjects used for evaluation, i.e subjects whose fixations
on images in predicted_filenumbers are taken for evaluation.
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
auc : area under the roc curve for sets of actuals and controls
true_pos_rate : ndarray
Rate of true positives for every given threshold value.
All values appearing in actuals are taken as thresholds. Uses lower
sum interpolation.
false_pos_rate : ndarray
See true_pos_rate but for false positives.
"""
predicting_fm = fm[
(ismember(fm.SUBJECTINDEX, predicting_subjects)) &
(ismember(fm.filenumber, predicting_filenumbers)) &
(fm.category == category)]
predicted_fm = fm[
(ismember(fm.SUBJECTINDEX,predicted_subjects)) &
(ismember(fm.filenumber,predicted_filenumbers))&
(fm.category == category)]
try:
predicting_fdm = compute_fdm(predicting_fm, scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
if controls == True:
fm_controls = fm[
(ismember(fm.SUBJECTINDEX, predicted_subjects)) &
((ismember(fm.filenumber, predicted_filenumbers)) != True) &
(fm.category == category)]
return measures.prediction_scores(predicting_fdm, predicted_fm,
controls = (fm_controls.y, fm_controls.x))
return measures.prediction_scores(predicting_fdm, predicted_fm, controls = None)
|
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Calculates how well the fixations from a set of subjects on a set of
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The prediction is carried out by computing a fixation density map from
fixations of predicting_subjects subjects on predicting_images images.
Prediction accuracy is assessed by measures.prediction_scores.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
predicting_filenumbers : list
List of filenumbers used for prediction, i.e. images where fixations
for the prediction are taken from.
predicting_subjects : list
List of subjects whose fixations on images in predicting_filenumbers
are used for the prediction.
predicted_filenumnbers : list
List of images from which the to be predicted fixations are taken.
predicted_subjects : list
List of subjects used for evaluation, i.e subjects whose fixations
on images in predicted_filenumbers are taken for evaluation.
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
auc : area under the roc curve for sets of actuals and controls
true_pos_rate : ndarray
Rate of true positives for every given threshold value.
All values appearing in actuals are taken as thresholds. Uses lower
sum interpolation.
false_pos_rate : ndarray
See true_pos_rate but for false positives.
|
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"subjects",
"on",
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"of",
"images",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/bounds.py#L12-L76
|
nwilming/ocupy
|
ocupy/bounds.py
|
intersubject_scores_random_subjects
|
def intersubject_scores_random_subjects(fm, category, filenumber, n_train,
n_predict, controls=True,
scale_factor = 1):
"""
Calculates how well the fixations of n random subjects on one image can
be predicted with the fixations of m other random subjects.
Notes
Function that uses intersubject_auc for computing auc.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
filnumber : int
Image from which fixations are taken.
n_train : int
The number of subjects which are used for prediction.
n_predict : int
The number of subjects to predict
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
tuple : prediction scores
"""
subjects = np.unique(fm.SUBJECTINDEX)
if len(subjects) < n_train + n_predict:
raise ValueError("""Not enough subjects in fixmat""")
# draw a random sample of subjects for testing and evaluation, according
# to the specified set sizes (n_train, n_predict)
np.random.shuffle(subjects)
predicted_subjects = subjects[0 : n_predict]
predicting_subjects = subjects[n_predict : n_predict + n_train]
assert len(predicting_subjects) == n_train
assert len(predicted_subjects) == n_predict
assert [x not in predicting_subjects for x in predicted_subjects]
return intersubject_scores(fm, category, [filenumber], predicting_subjects,
[filenumber], predicted_subjects,
controls, scale_factor)
|
python
|
def intersubject_scores_random_subjects(fm, category, filenumber, n_train,
n_predict, controls=True,
scale_factor = 1):
"""
Calculates how well the fixations of n random subjects on one image can
be predicted with the fixations of m other random subjects.
Notes
Function that uses intersubject_auc for computing auc.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
filnumber : int
Image from which fixations are taken.
n_train : int
The number of subjects which are used for prediction.
n_predict : int
The number of subjects to predict
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
tuple : prediction scores
"""
subjects = np.unique(fm.SUBJECTINDEX)
if len(subjects) < n_train + n_predict:
raise ValueError("""Not enough subjects in fixmat""")
# draw a random sample of subjects for testing and evaluation, according
# to the specified set sizes (n_train, n_predict)
np.random.shuffle(subjects)
predicted_subjects = subjects[0 : n_predict]
predicting_subjects = subjects[n_predict : n_predict + n_train]
assert len(predicting_subjects) == n_train
assert len(predicted_subjects) == n_predict
assert [x not in predicting_subjects for x in predicted_subjects]
return intersubject_scores(fm, category, [filenumber], predicting_subjects,
[filenumber], predicted_subjects,
controls, scale_factor)
|
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Calculates how well the fixations of n random subjects on one image can
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Notes
Function that uses intersubject_auc for computing auc.
Parameters
fm : fixmat instance
category : int
Category from which the fixations are taken.
filnumber : int
Image from which fixations are taken.
n_train : int
The number of subjects which are used for prediction.
n_predict : int
The number of subjects to predict
controls : bool, optional
If True (default), n_predict subjects are chosen from the fixmat.
If False, 1000 fixations are randomly generated and used for
testing.
scale_factor : int, optional
specifies the scaling of the fdm. Default is 1.
Returns
tuple : prediction scores
|
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/bounds.py#L78-L121
|
nwilming/ocupy
|
ocupy/bounds.py
|
upper_bound
|
def upper_bound(fm, nr_subs = None, scale_factor = 1):
"""
compute the inter-subject consistency upper bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of scores; the list contains one dictionary for each measure.
Each dictionary contains one key for each category and corresponding
values is an array with scores for each subject.
"""
nr_subs_total = len(np.unique(fm.SUBJECTINDEX))
if not nr_subs:
nr_subs = nr_subs_total - 1
assert (nr_subs < nr_subs_total)
# initialize output structure; every measure gets one dict with
# category numbers as keys and numpy-arrays as values
intersub_scores = []
for measure in range(len(measures.scores)):
res_dict = {}
result_vectors = [np.empty(nr_subs_total) + np.nan
for _ in np.unique(fm.category)]
res_dict.update(list(zip(np.unique(fm.category), result_vectors)))
intersub_scores.append(res_dict)
#compute inter-subject scores for every stimulus, with leave-one-out
#over subjects
for fm_cat in fm.by_field('category'):
cat = fm_cat.category[0]
for (sub_counter, sub) in enumerate(np.unique(fm_cat.SUBJECTINDEX)):
image_scores = []
for fm_single in fm_cat.by_field('filenumber'):
predicting_subs = (np.setdiff1d(np.unique(
fm_single.SUBJECTINDEX),[sub]))
np.random.shuffle(predicting_subs)
predicting_subs = predicting_subs[0:nr_subs]
predicting_fm = fm_single[
(ismember(fm_single.SUBJECTINDEX, predicting_subs))]
predicted_fm = fm_single[fm_single.SUBJECTINDEX == sub]
try:
predicting_fdm = compute_fdm(predicting_fm,
scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
image_scores.append(measures.prediction_scores(
predicting_fdm, predicted_fm))
for (measure, score) in enumerate(nanmean(image_scores, 0)):
intersub_scores[measure][cat][sub_counter] = score
return intersub_scores
|
python
|
def upper_bound(fm, nr_subs = None, scale_factor = 1):
"""
compute the inter-subject consistency upper bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of scores; the list contains one dictionary for each measure.
Each dictionary contains one key for each category and corresponding
values is an array with scores for each subject.
"""
nr_subs_total = len(np.unique(fm.SUBJECTINDEX))
if not nr_subs:
nr_subs = nr_subs_total - 1
assert (nr_subs < nr_subs_total)
# initialize output structure; every measure gets one dict with
# category numbers as keys and numpy-arrays as values
intersub_scores = []
for measure in range(len(measures.scores)):
res_dict = {}
result_vectors = [np.empty(nr_subs_total) + np.nan
for _ in np.unique(fm.category)]
res_dict.update(list(zip(np.unique(fm.category), result_vectors)))
intersub_scores.append(res_dict)
#compute inter-subject scores for every stimulus, with leave-one-out
#over subjects
for fm_cat in fm.by_field('category'):
cat = fm_cat.category[0]
for (sub_counter, sub) in enumerate(np.unique(fm_cat.SUBJECTINDEX)):
image_scores = []
for fm_single in fm_cat.by_field('filenumber'):
predicting_subs = (np.setdiff1d(np.unique(
fm_single.SUBJECTINDEX),[sub]))
np.random.shuffle(predicting_subs)
predicting_subs = predicting_subs[0:nr_subs]
predicting_fm = fm_single[
(ismember(fm_single.SUBJECTINDEX, predicting_subs))]
predicted_fm = fm_single[fm_single.SUBJECTINDEX == sub]
try:
predicting_fdm = compute_fdm(predicting_fm,
scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
image_scores.append(measures.prediction_scores(
predicting_fdm, predicted_fm))
for (measure, score) in enumerate(nanmean(image_scores, 0)):
intersub_scores[measure][cat][sub_counter] = score
return intersub_scores
|
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compute the inter-subject consistency upper bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of scores; the list contains one dictionary for each measure.
Each dictionary contains one key for each category and corresponding
values is an array with scores for each subject.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/bounds.py#L123-L173
|
nwilming/ocupy
|
ocupy/bounds.py
|
lower_bound
|
def lower_bound(fm, nr_subs = None, nr_imgs = None, scale_factor = 1):
"""
Compute the spatial bias lower bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
nr_imgs : the number of images used for prediction. If given, the
same number will be used for every category. If not given,
leave-one-out will be used in all categories.
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of spatial bias scores; the list contains one dictionary for each
measure. Each dictionary contains one key for each category and
corresponding values is an array with scores for each subject.
"""
nr_subs_total = len(np.unique(fm.SUBJECTINDEX))
if nr_subs is None:
nr_subs = nr_subs_total - 1
assert (nr_subs < nr_subs_total)
# initialize output structure; every measure gets one dict with
# category numbers as keys and numpy-arrays as values
sb_scores = []
for measure in range(len(measures.scores)):
res_dict = {}
result_vectors = [np.empty(nr_subs_total) + np.nan
for _ in np.unique(fm.category)]
res_dict.update(list(zip(np.unique(fm.category),result_vectors)))
sb_scores.append(res_dict)
# compute mean spatial bias predictive power for all subjects in all
# categories
for fm_cat in fm.by_field('category'):
cat = fm_cat.category[0]
nr_imgs_cat = len(np.unique(fm_cat.filenumber))
if not nr_imgs:
nr_imgs_current = nr_imgs_cat - 1
else:
nr_imgs_current = nr_imgs
assert(nr_imgs_current < nr_imgs_cat)
for (sub_counter, sub) in enumerate(np.unique(fm.SUBJECTINDEX)):
image_scores = []
for fm_single in fm_cat.by_field('filenumber'):
# Iterating by field filenumber makes filenumbers
# in fm_single unique: Just take the first one to get the
# filenumber for this fixmat
fn = fm_single.filenumber[0]
predicting_subs = (np.setdiff1d(np.unique(
fm_cat.SUBJECTINDEX), [sub]))
np.random.shuffle(predicting_subs)
predicting_subs = predicting_subs[0:nr_subs]
predicting_fns = (np.setdiff1d(np.unique(
fm_cat.filenumber), [fn]))
np.random.shuffle(predicting_fns)
predicting_fns = predicting_fns[0:nr_imgs_current]
predicting_fm = fm_cat[
(ismember(fm_cat.SUBJECTINDEX, predicting_subs)) &
(ismember(fm_cat.filenumber, predicting_fns))]
predicted_fm = fm_single[fm_single.SUBJECTINDEX == sub]
try:
predicting_fdm = compute_fdm(predicting_fm,
scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
image_scores.append(measures.prediction_scores(predicting_fdm,
predicted_fm))
for (measure, score) in enumerate(nanmean(image_scores, 0)):
sb_scores[measure][cat][sub_counter] = score
return sb_scores
|
python
|
def lower_bound(fm, nr_subs = None, nr_imgs = None, scale_factor = 1):
"""
Compute the spatial bias lower bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
nr_imgs : the number of images used for prediction. If given, the
same number will be used for every category. If not given,
leave-one-out will be used in all categories.
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of spatial bias scores; the list contains one dictionary for each
measure. Each dictionary contains one key for each category and
corresponding values is an array with scores for each subject.
"""
nr_subs_total = len(np.unique(fm.SUBJECTINDEX))
if nr_subs is None:
nr_subs = nr_subs_total - 1
assert (nr_subs < nr_subs_total)
# initialize output structure; every measure gets one dict with
# category numbers as keys and numpy-arrays as values
sb_scores = []
for measure in range(len(measures.scores)):
res_dict = {}
result_vectors = [np.empty(nr_subs_total) + np.nan
for _ in np.unique(fm.category)]
res_dict.update(list(zip(np.unique(fm.category),result_vectors)))
sb_scores.append(res_dict)
# compute mean spatial bias predictive power for all subjects in all
# categories
for fm_cat in fm.by_field('category'):
cat = fm_cat.category[0]
nr_imgs_cat = len(np.unique(fm_cat.filenumber))
if not nr_imgs:
nr_imgs_current = nr_imgs_cat - 1
else:
nr_imgs_current = nr_imgs
assert(nr_imgs_current < nr_imgs_cat)
for (sub_counter, sub) in enumerate(np.unique(fm.SUBJECTINDEX)):
image_scores = []
for fm_single in fm_cat.by_field('filenumber'):
# Iterating by field filenumber makes filenumbers
# in fm_single unique: Just take the first one to get the
# filenumber for this fixmat
fn = fm_single.filenumber[0]
predicting_subs = (np.setdiff1d(np.unique(
fm_cat.SUBJECTINDEX), [sub]))
np.random.shuffle(predicting_subs)
predicting_subs = predicting_subs[0:nr_subs]
predicting_fns = (np.setdiff1d(np.unique(
fm_cat.filenumber), [fn]))
np.random.shuffle(predicting_fns)
predicting_fns = predicting_fns[0:nr_imgs_current]
predicting_fm = fm_cat[
(ismember(fm_cat.SUBJECTINDEX, predicting_subs)) &
(ismember(fm_cat.filenumber, predicting_fns))]
predicted_fm = fm_single[fm_single.SUBJECTINDEX == sub]
try:
predicting_fdm = compute_fdm(predicting_fm,
scale_factor = scale_factor)
except RuntimeError:
predicting_fdm = None
image_scores.append(measures.prediction_scores(predicting_fdm,
predicted_fm))
for (measure, score) in enumerate(nanmean(image_scores, 0)):
sb_scores[measure][cat][sub_counter] = score
return sb_scores
|
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Compute the spatial bias lower bound for a fixmat.
Input:
fm : a fixmat instance
nr_subs : the number of subjects used for the prediction. Defaults
to the total number of subjects in the fixmat minus 1
nr_imgs : the number of images used for prediction. If given, the
same number will be used for every category. If not given,
leave-one-out will be used in all categories.
scale_factor : the scale factor of the FDMs. Default is 1.
Returns:
A list of spatial bias scores; the list contains one dictionary for each
measure. Each dictionary contains one key for each category and
corresponding values is an array with scores for each subject.
|
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/bounds.py#L175-L243
|
nwilming/ocupy
|
ocupy/parallel.py
|
ind2sub
|
def ind2sub(ind, dimensions):
"""
Calculates subscripts for indices into regularly spaced matrixes.
"""
# check that the index is within range
if ind >= np.prod(dimensions):
raise RuntimeError("ind2sub: index exceeds array size")
cum_dims = list(dimensions)
cum_dims.reverse()
m = 1
mult = []
for d in cum_dims:
m = m*d
mult.append(m)
mult.pop()
mult.reverse()
mult.append(1)
indices = []
for d in mult:
indices.append((ind/d)+1)
ind = ind - (ind/d)*d
return indices
|
python
|
def ind2sub(ind, dimensions):
"""
Calculates subscripts for indices into regularly spaced matrixes.
"""
# check that the index is within range
if ind >= np.prod(dimensions):
raise RuntimeError("ind2sub: index exceeds array size")
cum_dims = list(dimensions)
cum_dims.reverse()
m = 1
mult = []
for d in cum_dims:
m = m*d
mult.append(m)
mult.pop()
mult.reverse()
mult.append(1)
indices = []
for d in mult:
indices.append((ind/d)+1)
ind = ind - (ind/d)*d
return indices
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L268-L289
|
nwilming/ocupy
|
ocupy/parallel.py
|
sub2ind
|
def sub2ind(indices, dimensions):
"""
An exemplary sub2ind implementation to create randomization
scripts.
This function calculates indices from subscripts into regularly spaced
matrixes.
"""
# check that none of the indices exceeds the size of the array
if any([i > j for i, j in zip(indices, dimensions)]):
raise RuntimeError("sub2ind:an index exceeds its dimension's size")
dims = list(dimensions)
dims.append(1)
dims.remove(dims[0])
dims.reverse()
ind = list(indices)
ind.reverse()
idx = 0
mult = 1
for (cnt, dim) in zip(ind, dims):
mult = dim*mult
idx = idx + (cnt-1)*mult
return idx
|
python
|
def sub2ind(indices, dimensions):
"""
An exemplary sub2ind implementation to create randomization
scripts.
This function calculates indices from subscripts into regularly spaced
matrixes.
"""
# check that none of the indices exceeds the size of the array
if any([i > j for i, j in zip(indices, dimensions)]):
raise RuntimeError("sub2ind:an index exceeds its dimension's size")
dims = list(dimensions)
dims.append(1)
dims.remove(dims[0])
dims.reverse()
ind = list(indices)
ind.reverse()
idx = 0
mult = 1
for (cnt, dim) in zip(ind, dims):
mult = dim*mult
idx = idx + (cnt-1)*mult
return idx
|
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[
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L292-L314
|
nwilming/ocupy
|
ocupy/parallel.py
|
RestoreTaskStoreFactory
|
def RestoreTaskStoreFactory(store_class, chunk_size, restore_file, save_file):
"""
Restores a task store from file.
"""
intm_results = np.load(restore_file)
intm = intm_results[intm_results.files[0]]
idx = np.isnan(intm).flatten().nonzero()[0]
partitions = math.ceil(len(idx) / float(chunk_size))
task_store = store_class(partitions, idx.tolist(), save_file)
task_store.num_tasks = len(idx)
# Also set up matrices for saving results
for f in intm_results.files:
task_store.__dict__[f] = intm_results[f]
return task_store
|
python
|
def RestoreTaskStoreFactory(store_class, chunk_size, restore_file, save_file):
"""
Restores a task store from file.
"""
intm_results = np.load(restore_file)
intm = intm_results[intm_results.files[0]]
idx = np.isnan(intm).flatten().nonzero()[0]
partitions = math.ceil(len(idx) / float(chunk_size))
task_store = store_class(partitions, idx.tolist(), save_file)
task_store.num_tasks = len(idx)
# Also set up matrices for saving results
for f in intm_results.files:
task_store.__dict__[f] = intm_results[f]
return task_store
|
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L316-L329
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskManager.xmlrpc_reschedule
|
def xmlrpc_reschedule(self):
"""
Reschedule all running tasks.
"""
if not len(self.scheduled_tasks) == 0:
self.reschedule = list(self.scheduled_tasks.items())
self.scheduled_tasks = {}
return True
|
python
|
def xmlrpc_reschedule(self):
"""
Reschedule all running tasks.
"""
if not len(self.scheduled_tasks) == 0:
self.reschedule = list(self.scheduled_tasks.items())
self.scheduled_tasks = {}
return True
|
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Reschedule all running tasks.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L61-L68
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskManager.xmlrpc_get_task
|
def xmlrpc_get_task(self):
"""
Return a new task description: ID and necessary parameters,
all are given in a dictionary
"""
try:
if len(self.reschedule) == 0:
(task_id, cur_task) = next(self.task_iterator)
else:
(task_id, cur_task) = self.reschedule.pop()
self.scheduled_tasks.update({task_id: cur_task})
return (task_id, cur_task.to_dict())
except StopIteration:
print('StopIteration: No more tasks')
return False
except Exception as err:
print('Some other error')
print(err)
return False
|
python
|
def xmlrpc_get_task(self):
"""
Return a new task description: ID and necessary parameters,
all are given in a dictionary
"""
try:
if len(self.reschedule) == 0:
(task_id, cur_task) = next(self.task_iterator)
else:
(task_id, cur_task) = self.reschedule.pop()
self.scheduled_tasks.update({task_id: cur_task})
return (task_id, cur_task.to_dict())
except StopIteration:
print('StopIteration: No more tasks')
return False
except Exception as err:
print('Some other error')
print(err)
return False
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L70-L88
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskManager.xmlrpc_task_done
|
def xmlrpc_task_done(self, result):
"""
Take the results of a computation and put it into the results list.
"""
(task_id, task_results) = result
del self.scheduled_tasks[task_id]
self.task_store.update_results(task_id, task_results)
self.results += 1
return True
|
python
|
def xmlrpc_task_done(self, result):
"""
Take the results of a computation and put it into the results list.
"""
(task_id, task_results) = result
del self.scheduled_tasks[task_id]
self.task_store.update_results(task_id, task_results)
self.results += 1
return True
|
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L90-L98
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskManager.xmlrpc_status
|
def xmlrpc_status(self):
"""
Return a status message
"""
return ("""
%i Jobs are still wating for execution
%i Jobs are being processed
%i Jobs are done
""" %(self.task_store.partitions -
self.results -
len(self.scheduled_tasks),
len(self.scheduled_tasks),
self.results))
|
python
|
def xmlrpc_status(self):
"""
Return a status message
"""
return ("""
%i Jobs are still wating for execution
%i Jobs are being processed
%i Jobs are done
""" %(self.task_store.partitions -
self.results -
len(self.scheduled_tasks),
len(self.scheduled_tasks),
self.results))
|
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"(",
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Return a status message
|
[
"Return",
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"status",
"message"
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L100-L112
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskManager.xmlrpc_save2file
|
def xmlrpc_save2file(self, filename):
"""
Save results and own state into file.
"""
savefile = open(filename,'wb')
try:
pickle.dump({'scheduled':self.scheduled_tasks,
'reschedule':self.reschedule},savefile)
except pickle.PicklingError:
return -1
savefile.close()
return 1
|
python
|
def xmlrpc_save2file(self, filename):
"""
Save results and own state into file.
"""
savefile = open(filename,'wb')
try:
pickle.dump({'scheduled':self.scheduled_tasks,
'reschedule':self.reschedule},savefile)
except pickle.PicklingError:
return -1
savefile.close()
return 1
|
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Save results and own state into file.
|
[
"Save",
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"state",
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"file",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L114-L125
|
nwilming/ocupy
|
ocupy/parallel.py
|
Worker.run
|
def run(self):
"""This function needs to be called to start the computation."""
(task_id, tasks) = self.server.get_task()
self.task_store.from_dict(tasks)
for (index, task) in self.task_store:
result = self.compute(index, task)
self.results.append(result)
self.server.task_done((task_id, self.results))
|
python
|
def run(self):
"""This function needs to be called to start the computation."""
(task_id, tasks) = self.server.get_task()
self.task_store.from_dict(tasks)
for (index, task) in self.task_store:
result = self.compute(index, task)
self.results.append(result)
self.server.task_done((task_id, self.results))
|
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|
[
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] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L158-L165
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskStore.from_dict
|
def from_dict(self, description):
"""Configures the task store to be the task_store described
in description"""
assert(self.ident == description['ident'])
self.partitions = description['partitions']
self.indices = description['indices']
|
python
|
def from_dict(self, description):
"""Configures the task store to be the task_store described
in description"""
assert(self.ident == description['ident'])
self.partitions = description['partitions']
self.indices = description['indices']
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L216-L221
|
nwilming/ocupy
|
ocupy/parallel.py
|
TaskStore.partition
|
def partition(self):
"""Partitions all tasks into groups of tasks. A group is
represented by a task_store object that indexes a sub-
set of tasks."""
step = int(math.ceil(self.num_tasks / float(self.partitions)))
if self.indices == None:
slice_ind = list(range(0, self.num_tasks, step))
for start in slice_ind:
yield self.__class__(self.partitions,
list(range(start, start + step)))
else:
slice_ind = list(range(0, len(self.indices), step))
for start in slice_ind:
if start + step <= len(self.indices):
yield self.__class__(self.partitions,
self.indices[start: start + step])
else:
yield self.__class__(self.partitions, self.indices[start:])
|
python
|
def partition(self):
"""Partitions all tasks into groups of tasks. A group is
represented by a task_store object that indexes a sub-
set of tasks."""
step = int(math.ceil(self.num_tasks / float(self.partitions)))
if self.indices == None:
slice_ind = list(range(0, self.num_tasks, step))
for start in slice_ind:
yield self.__class__(self.partitions,
list(range(start, start + step)))
else:
slice_ind = list(range(0, len(self.indices), step))
for start in slice_ind:
if start + step <= len(self.indices):
yield self.__class__(self.partitions,
self.indices[start: start + step])
else:
yield self.__class__(self.partitions, self.indices[start:])
|
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|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/parallel.py#L228-L245
|
nwilming/ocupy
|
ocupy/spline_base.py
|
fit3d
|
def fit3d(samples, e_x, e_y, e_z, remove_zeros = False, **kw):
"""Fits a 3D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
"""
height, width, depth = len(e_y)-1, len(e_x)-1, len(e_z)-1
(p_est, _) = np.histogramdd(samples, (e_x, e_y, e_z))
p_est = p_est/sum(p_est.flat)
p_est = p_est.flatten()
if remove_zeros:
non_zero = ~(p_est == 0)
else:
non_zero = (p_est >= 0)
basis = spline_base3d(width,height, depth, **kw)
model = linear_model.BayesianRidge()
model.fit(basis[:, non_zero].T, p_est[:,np.newaxis][non_zero,:])
return (model.predict(basis.T).reshape((width, height, depth)),
p_est.reshape((width, height, depth)))
|
python
|
def fit3d(samples, e_x, e_y, e_z, remove_zeros = False, **kw):
"""Fits a 3D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
"""
height, width, depth = len(e_y)-1, len(e_x)-1, len(e_z)-1
(p_est, _) = np.histogramdd(samples, (e_x, e_y, e_z))
p_est = p_est/sum(p_est.flat)
p_est = p_est.flatten()
if remove_zeros:
non_zero = ~(p_est == 0)
else:
non_zero = (p_est >= 0)
basis = spline_base3d(width,height, depth, **kw)
model = linear_model.BayesianRidge()
model.fit(basis[:, non_zero].T, p_est[:,np.newaxis][non_zero,:])
return (model.predict(basis.T).reshape((width, height, depth)),
p_est.reshape((width, height, depth)))
|
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Fits a 3D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
|
[
"Fits",
"a",
"3D",
"distribution",
"with",
"splines",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L9-L48
|
nwilming/ocupy
|
ocupy/spline_base.py
|
fit2d
|
def fit2d(samples,e_x, e_y, remove_zeros = False, p_est = None, **kw):
"""Fits a 2D distribution with splines.
Input:
samples: Matrix or list of arrays
If matrix, it must be of size Nx2, where N is the number of
observations. If list, it must contain two arrays of length
N.
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
"""
if p_est is None:
height = len(e_y)-1
width = len(e_x)-1
(p_est, _) = np.histogramdd(samples, (e_x, e_y))
else:
p_est = p_est.T
width, height = p_est.shape
# p_est contains x in dim 1 and y in dim 0
shape = p_est.shape
p_est = (p_est/sum(p_est.flat)).reshape(shape)
mx = p_est.sum(1)
my = p_est.sum(0)
# Transpose hist to have x in dim 0
p_est = p_est.T.flatten()
basis, knots = spline_base2d(width, height, marginal_x = mx, marginal_y = my, **kw)
model = linear_model.BayesianRidge()
if remove_zeros:
non_zero = ~(p_est == 0)
model.fit(basis[:, non_zero].T, p_est[non_zero])
else:
non_zero = (p_est >= 0)
p_est[~non_zero,:] = np.finfo(float).eps
model.fit(basis.T, p_est)
return (model.predict(basis.T).reshape((height, width)),
p_est.reshape((height, width)), knots)
|
python
|
def fit2d(samples,e_x, e_y, remove_zeros = False, p_est = None, **kw):
"""Fits a 2D distribution with splines.
Input:
samples: Matrix or list of arrays
If matrix, it must be of size Nx2, where N is the number of
observations. If list, it must contain two arrays of length
N.
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
"""
if p_est is None:
height = len(e_y)-1
width = len(e_x)-1
(p_est, _) = np.histogramdd(samples, (e_x, e_y))
else:
p_est = p_est.T
width, height = p_est.shape
# p_est contains x in dim 1 and y in dim 0
shape = p_est.shape
p_est = (p_est/sum(p_est.flat)).reshape(shape)
mx = p_est.sum(1)
my = p_est.sum(0)
# Transpose hist to have x in dim 0
p_est = p_est.T.flatten()
basis, knots = spline_base2d(width, height, marginal_x = mx, marginal_y = my, **kw)
model = linear_model.BayesianRidge()
if remove_zeros:
non_zero = ~(p_est == 0)
model.fit(basis[:, non_zero].T, p_est[non_zero])
else:
non_zero = (p_est >= 0)
p_est[~non_zero,:] = np.finfo(float).eps
model.fit(basis.T, p_est)
return (model.predict(basis.T).reshape((height, width)),
p_est.reshape((height, width)), knots)
|
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Fits a 2D distribution with splines.
Input:
samples: Matrix or list of arrays
If matrix, it must be of size Nx2, where N is the number of
observations. If list, it must contain two arrays of length
N.
e_x: Array
Edges that define the events in the probability
distribution along the x direction. For example,
e_x[0] < samples[0] <= e_x[1] picks out all
samples that are associated with the first event.
e_y: Array
See e_x, but for the y direction.
remove_zeros: Bool
If True, events that are not observed will not
be part of the fitting process. If False, those
events will be modelled as finfo('float').eps
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Tuple of arrays
Sequence of knots that were used for the spline basis (x,y)
|
[
"Fits",
"a",
"2D",
"distribution",
"with",
"splines",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L51-L103
|
nwilming/ocupy
|
ocupy/spline_base.py
|
fit1d
|
def fit1d(samples, e, remove_zeros = False, **kw):
"""Fits a 1D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e: Array
Edges that define the events in the probability
distribution. For example, e[0] < x <= e[1] is
the range of values that are associated with the
first event.
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Array
Sequence of knots that were used for the spline basis
"""
samples = samples[~np.isnan(samples)]
length = len(e)-1
hist,_ = np.histogramdd(samples, (e,))
hist = hist/sum(hist)
basis, knots = spline_base1d(length, marginal = hist, **kw)
non_zero = hist>0
model = linear_model.BayesianRidge()
if remove_zeros:
model.fit(basis[non_zero, :], hist[:,np.newaxis][non_zero,:])
else:
hist[~non_zero] = np.finfo(float).eps
model.fit(basis, hist[:,np.newaxis])
return model.predict(basis), hist, knots
|
python
|
def fit1d(samples, e, remove_zeros = False, **kw):
"""Fits a 1D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e: Array
Edges that define the events in the probability
distribution. For example, e[0] < x <= e[1] is
the range of values that are associated with the
first event.
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Array
Sequence of knots that were used for the spline basis
"""
samples = samples[~np.isnan(samples)]
length = len(e)-1
hist,_ = np.histogramdd(samples, (e,))
hist = hist/sum(hist)
basis, knots = spline_base1d(length, marginal = hist, **kw)
non_zero = hist>0
model = linear_model.BayesianRidge()
if remove_zeros:
model.fit(basis[non_zero, :], hist[:,np.newaxis][non_zero,:])
else:
hist[~non_zero] = np.finfo(float).eps
model.fit(basis, hist[:,np.newaxis])
return model.predict(basis), hist, knots
|
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Fits a 1D distribution with splines.
Input:
samples: Array
Array of samples from a probability distribution
e: Array
Edges that define the events in the probability
distribution. For example, e[0] < x <= e[1] is
the range of values that are associated with the
first event.
**kw: Arguments that are passed on to spline_bse1d.
Returns:
distribution: Array
An array that gives an estimate of probability for
events defined by e.
knots: Array
Sequence of knots that were used for the spline basis
|
[
"Fits",
"a",
"1D",
"distribution",
"with",
"splines",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L105-L137
|
nwilming/ocupy
|
ocupy/spline_base.py
|
knots_from_marginal
|
def knots_from_marginal(marginal, nr_knots, spline_order):
"""
Determines knot placement based on a marginal distribution.
It places knots such that each knot covers the same amount
of probability mass. Two of the knots are reserved for the
borders which are treated seperatly. For example, a uniform
distribution with 5 knots will cause the knots to be equally
spaced with 25% of the probability mass between each two
knots.
Input:
marginal: Array
Estimate of the marginal distribution used to estimate
knot placement.
nr_knots: int
Number of knots to be placed.
spline_order: int
Order of the splines
Returns:
knots: Array
Sequence of knot positions
"""
cumsum = np.cumsum(marginal)
cumsum = cumsum/cumsum.max()
borders = np.linspace(0,1,nr_knots)
knot_placement = [0] + np.unique([np.where(cumsum>=b)[0][0] for b in borders[1:-1]]).tolist() +[len(marginal)-1]
knots = augknt(knot_placement, spline_order)
return knots
|
python
|
def knots_from_marginal(marginal, nr_knots, spline_order):
"""
Determines knot placement based on a marginal distribution.
It places knots such that each knot covers the same amount
of probability mass. Two of the knots are reserved for the
borders which are treated seperatly. For example, a uniform
distribution with 5 knots will cause the knots to be equally
spaced with 25% of the probability mass between each two
knots.
Input:
marginal: Array
Estimate of the marginal distribution used to estimate
knot placement.
nr_knots: int
Number of knots to be placed.
spline_order: int
Order of the splines
Returns:
knots: Array
Sequence of knot positions
"""
cumsum = np.cumsum(marginal)
cumsum = cumsum/cumsum.max()
borders = np.linspace(0,1,nr_knots)
knot_placement = [0] + np.unique([np.where(cumsum>=b)[0][0] for b in borders[1:-1]]).tolist() +[len(marginal)-1]
knots = augknt(knot_placement, spline_order)
return knots
|
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Determines knot placement based on a marginal distribution.
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of probability mass. Two of the knots are reserved for the
borders which are treated seperatly. For example, a uniform
distribution with 5 knots will cause the knots to be equally
spaced with 25% of the probability mass between each two
knots.
Input:
marginal: Array
Estimate of the marginal distribution used to estimate
knot placement.
nr_knots: int
Number of knots to be placed.
spline_order: int
Order of the splines
Returns:
knots: Array
Sequence of knot positions
|
[
"Determines",
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"a",
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"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L139-L168
|
nwilming/ocupy
|
ocupy/spline_base.py
|
spline_base1d
|
def spline_base1d(length, nr_knots = 20, spline_order = 5, marginal = None):
"""Computes a 1D spline basis
Input:
length: int
length of each basis
nr_knots: int
Number of knots, i.e. number of basis functions.
spline_order: int
Order of the splines.
marginal: array, optional
Estimate of the marginal distribution of the input to be fitted.
If given, it is used to determine the positioning of knots, each
knot will cover the same amount of probability mass. If not given,
knots are equally spaced.
"""
if marginal is None:
knots = augknt(np.linspace(0,length+1, nr_knots), spline_order)
else:
knots = knots_from_marginal(marginal, nr_knots, spline_order)
x_eval = np.arange(1,length+1).astype(float)
Bsplines = spcol(x_eval,knots,spline_order)
return Bsplines, knots
|
python
|
def spline_base1d(length, nr_knots = 20, spline_order = 5, marginal = None):
"""Computes a 1D spline basis
Input:
length: int
length of each basis
nr_knots: int
Number of knots, i.e. number of basis functions.
spline_order: int
Order of the splines.
marginal: array, optional
Estimate of the marginal distribution of the input to be fitted.
If given, it is used to determine the positioning of knots, each
knot will cover the same amount of probability mass. If not given,
knots are equally spaced.
"""
if marginal is None:
knots = augknt(np.linspace(0,length+1, nr_knots), spline_order)
else:
knots = knots_from_marginal(marginal, nr_knots, spline_order)
x_eval = np.arange(1,length+1).astype(float)
Bsplines = spcol(x_eval,knots,spline_order)
return Bsplines, knots
|
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Computes a 1D spline basis
Input:
length: int
length of each basis
nr_knots: int
Number of knots, i.e. number of basis functions.
spline_order: int
Order of the splines.
marginal: array, optional
Estimate of the marginal distribution of the input to be fitted.
If given, it is used to determine the positioning of knots, each
knot will cover the same amount of probability mass. If not given,
knots are equally spaced.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L171-L194
|
nwilming/ocupy
|
ocupy/spline_base.py
|
spline_base2d
|
def spline_base2d(width, height, nr_knots_x = 20.0, nr_knots_y = 20.0,
spline_order = 5, marginal_x = None, marginal_y = None):
"""Computes a set of 2D spline basis functions.
The basis functions cover the entire space in height*width and can
for example be used to create fixation density maps.
Input:
width: int
width of each basis
height: int
height of each basis
nr_knots_x: int
of knots in x (width) direction.
nr_knots_y: int
of knots in y (height) direction.
spline_order: int
Order of the spline.
marginal_x: array, optional
Estimate of marginal distribution of the input to be fitted
along the x-direction (width). If given, it is used to determine
the positioning of knots, each knot will cover the same amount
of probability mass. If not given, knots are equally spaced.
marginal_y: array, optional
Marginal distribution along the y-direction (height). If
given, it is used to determine the positioning of knots.
Each knot will cover the same amount of probability mass.
Output:
basis: Matrix
Matrix of size n*(width*height) that contains in each row
one vectorized basis.
knots: Tuple
(x,y) are knot arrays that show the placement of knots.
"""
if not (nr_knots_x<width and nr_knots_y<height):
raise RuntimeError("Too many knots for size of the base")
if marginal_x is None:
knots_x = augknt(np.linspace(0,width+1,nr_knots_x), spline_order)
else:
knots_x = knots_from_marginal(marginal_x, nr_knots_x, spline_order)
if marginal_y is None:
knots_y = augknt(np.linspace(0,height+1, nr_knots_y), spline_order)
else:
knots_y = knots_from_marginal(marginal_y, nr_knots_y, spline_order)
x_eval = np.arange(1,width+1).astype(float)
y_eval = np.arange(1,height+1).astype(float)
spline_setx = spcol(x_eval, knots_x, spline_order)
spline_sety = spcol(y_eval, knots_y, spline_order)
nr_coeff = [spline_sety.shape[1], spline_setx.shape[1]]
dim_bspline = [nr_coeff[0]*nr_coeff[1], len(x_eval)*len(y_eval)]
# construct 2D B-splines
nr_basis = 0
bspline = np.zeros(dim_bspline)
for IDX1 in range(0,nr_coeff[0]):
for IDX2 in range(0, nr_coeff[1]):
rand_coeff = np.zeros((nr_coeff[0] , nr_coeff[1]))
rand_coeff[IDX1,IDX2] = 1
tmp = np.dot(spline_sety,rand_coeff)
bspline[nr_basis,:] = np.dot(tmp,spline_setx.T).reshape((1,-1))
nr_basis = nr_basis+1
return bspline, (knots_x, knots_y)
|
python
|
def spline_base2d(width, height, nr_knots_x = 20.0, nr_knots_y = 20.0,
spline_order = 5, marginal_x = None, marginal_y = None):
"""Computes a set of 2D spline basis functions.
The basis functions cover the entire space in height*width and can
for example be used to create fixation density maps.
Input:
width: int
width of each basis
height: int
height of each basis
nr_knots_x: int
of knots in x (width) direction.
nr_knots_y: int
of knots in y (height) direction.
spline_order: int
Order of the spline.
marginal_x: array, optional
Estimate of marginal distribution of the input to be fitted
along the x-direction (width). If given, it is used to determine
the positioning of knots, each knot will cover the same amount
of probability mass. If not given, knots are equally spaced.
marginal_y: array, optional
Marginal distribution along the y-direction (height). If
given, it is used to determine the positioning of knots.
Each knot will cover the same amount of probability mass.
Output:
basis: Matrix
Matrix of size n*(width*height) that contains in each row
one vectorized basis.
knots: Tuple
(x,y) are knot arrays that show the placement of knots.
"""
if not (nr_knots_x<width and nr_knots_y<height):
raise RuntimeError("Too many knots for size of the base")
if marginal_x is None:
knots_x = augknt(np.linspace(0,width+1,nr_knots_x), spline_order)
else:
knots_x = knots_from_marginal(marginal_x, nr_knots_x, spline_order)
if marginal_y is None:
knots_y = augknt(np.linspace(0,height+1, nr_knots_y), spline_order)
else:
knots_y = knots_from_marginal(marginal_y, nr_knots_y, spline_order)
x_eval = np.arange(1,width+1).astype(float)
y_eval = np.arange(1,height+1).astype(float)
spline_setx = spcol(x_eval, knots_x, spline_order)
spline_sety = spcol(y_eval, knots_y, spline_order)
nr_coeff = [spline_sety.shape[1], spline_setx.shape[1]]
dim_bspline = [nr_coeff[0]*nr_coeff[1], len(x_eval)*len(y_eval)]
# construct 2D B-splines
nr_basis = 0
bspline = np.zeros(dim_bspline)
for IDX1 in range(0,nr_coeff[0]):
for IDX2 in range(0, nr_coeff[1]):
rand_coeff = np.zeros((nr_coeff[0] , nr_coeff[1]))
rand_coeff[IDX1,IDX2] = 1
tmp = np.dot(spline_sety,rand_coeff)
bspline[nr_basis,:] = np.dot(tmp,spline_setx.T).reshape((1,-1))
nr_basis = nr_basis+1
return bspline, (knots_x, knots_y)
|
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width: int
width of each basis
height: int
height of each basis
nr_knots_x: int
of knots in x (width) direction.
nr_knots_y: int
of knots in y (height) direction.
spline_order: int
Order of the spline.
marginal_x: array, optional
Estimate of marginal distribution of the input to be fitted
along the x-direction (width). If given, it is used to determine
the positioning of knots, each knot will cover the same amount
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marginal_y: array, optional
Marginal distribution along the y-direction (height). If
given, it is used to determine the positioning of knots.
Each knot will cover the same amount of probability mass.
Output:
basis: Matrix
Matrix of size n*(width*height) that contains in each row
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knots: Tuple
(x,y) are knot arrays that show the placement of knots.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L197-L257
|
nwilming/ocupy
|
ocupy/spline_base.py
|
spline_base3d
|
def spline_base3d( width, height, depth, nr_knots_x = 10.0, nr_knots_y = 10.0,
nr_knots_z=10, spline_order = 3, marginal_x = None, marginal_y = None,
marginal_z = None):
"""Computes a set of 3D spline basis functions.
For a description of the parameters see spline_base2d.
"""
if not nr_knots_z < depth:
raise RuntimeError("Too many knots for size of the base")
basis2d, (knots_x, knots_y) = spline_base2d(height, width, nr_knots_x,
nr_knots_y, spline_order, marginal_x, marginal_y)
if marginal_z is not None:
knots_z = knots_from_marginal(marginal_z, nr_knots_z, spline_order)
else:
knots_z = augknt(np.linspace(0,depth+1, nr_knots_z), spline_order)
z_eval = np.arange(1,depth+1).astype(float)
spline_setz = spcol(z_eval, knots_z, spline_order)
bspline = np.zeros((basis2d.shape[0]*len(z_eval), height*width*depth))
basis_nr = 0
for spline_a in spline_setz.T:
for spline_b in basis2d:
spline_b = spline_b.reshape((height, width))
bspline[basis_nr, :] = (spline_b[:,:,np.newaxis] * spline_a[:]).flat
basis_nr +=1
return bspline, (knots_x, knots_y, knots_z)
|
python
|
def spline_base3d( width, height, depth, nr_knots_x = 10.0, nr_knots_y = 10.0,
nr_knots_z=10, spline_order = 3, marginal_x = None, marginal_y = None,
marginal_z = None):
"""Computes a set of 3D spline basis functions.
For a description of the parameters see spline_base2d.
"""
if not nr_knots_z < depth:
raise RuntimeError("Too many knots for size of the base")
basis2d, (knots_x, knots_y) = spline_base2d(height, width, nr_knots_x,
nr_knots_y, spline_order, marginal_x, marginal_y)
if marginal_z is not None:
knots_z = knots_from_marginal(marginal_z, nr_knots_z, spline_order)
else:
knots_z = augknt(np.linspace(0,depth+1, nr_knots_z), spline_order)
z_eval = np.arange(1,depth+1).astype(float)
spline_setz = spcol(z_eval, knots_z, spline_order)
bspline = np.zeros((basis2d.shape[0]*len(z_eval), height*width*depth))
basis_nr = 0
for spline_a in spline_setz.T:
for spline_b in basis2d:
spline_b = spline_b.reshape((height, width))
bspline[basis_nr, :] = (spline_b[:,:,np.newaxis] * spline_a[:]).flat
basis_nr +=1
return bspline, (knots_x, knots_y, knots_z)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L259-L283
|
nwilming/ocupy
|
ocupy/spline_base.py
|
spline
|
def spline(x,knots,p,i=0.0):
"""Evaluates the ith spline basis given by knots on points in x"""
assert(p+1<len(knots))
return np.array([N(float(u),float(i),float(p),knots) for u in x])
|
python
|
def spline(x,knots,p,i=0.0):
"""Evaluates the ith spline basis given by knots on points in x"""
assert(p+1<len(knots))
return np.array([N(float(u),float(i),float(p),knots) for u in x])
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L285-L288
|
nwilming/ocupy
|
ocupy/spline_base.py
|
spcol
|
def spcol(x,knots,spline_order):
"""Computes the spline colocation matrix for knots in x.
The spline collocation matrix contains all m-p-1 bases
defined by knots. Specifically it contains the ith basis
in the ith column.
Input:
x: vector to evaluate the bases on
knots: vector of knots
spline_order: order of the spline
Output:
colmat: m x m-p matrix
The colocation matrix has size m x m-p where m
denotes the number of points the basis is evaluated
on and p is the spline order. The colums contain
the ith basis of knots evaluated on x.
"""
colmat = np.nan*np.ones((len(x),len(knots) - spline_order-1))
for i in range(0,len(knots) - spline_order -1):
colmat[:,i] = spline(x,knots,spline_order,i)
return colmat
|
python
|
def spcol(x,knots,spline_order):
"""Computes the spline colocation matrix for knots in x.
The spline collocation matrix contains all m-p-1 bases
defined by knots. Specifically it contains the ith basis
in the ith column.
Input:
x: vector to evaluate the bases on
knots: vector of knots
spline_order: order of the spline
Output:
colmat: m x m-p matrix
The colocation matrix has size m x m-p where m
denotes the number of points the basis is evaluated
on and p is the spline order. The colums contain
the ith basis of knots evaluated on x.
"""
colmat = np.nan*np.ones((len(x),len(knots) - spline_order-1))
for i in range(0,len(knots) - spline_order -1):
colmat[:,i] = spline(x,knots,spline_order,i)
return colmat
|
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Computes the spline colocation matrix for knots in x.
The spline collocation matrix contains all m-p-1 bases
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Input:
x: vector to evaluate the bases on
knots: vector of knots
spline_order: order of the spline
Output:
colmat: m x m-p matrix
The colocation matrix has size m x m-p where m
denotes the number of points the basis is evaluated
on and p is the spline order. The colums contain
the ith basis of knots evaluated on x.
|
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"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L290-L311
|
nwilming/ocupy
|
ocupy/spline_base.py
|
augknt
|
def augknt(knots,order):
"""Augment knot sequence such that some boundary conditions
are met."""
a = []
[a.append(knots[0]) for t in range(0,order)]
[a.append(k) for k in knots]
[a.append(knots[-1]) for t in range(0,order)]
return np.array(a)
|
python
|
def augknt(knots,order):
"""Augment knot sequence such that some boundary conditions
are met."""
a = []
[a.append(knots[0]) for t in range(0,order)]
[a.append(k) for k in knots]
[a.append(knots[-1]) for t in range(0,order)]
return np.array(a)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L313-L320
|
nwilming/ocupy
|
ocupy/spline_base.py
|
N
|
def N(u,i,p,knots):
"""Compute Spline Basis
Evaluates the spline basis of order p defined by knots
at knot i and point u.
"""
if p == 0:
if knots[i] < u and u <=knots[i+1]:
return 1.0
else:
return 0.0
else:
try:
k = (( float((u-knots[i]))/float((knots[i+p] - knots[i]) ))
* N(u,i,p-1,knots))
except ZeroDivisionError:
k = 0.0
try:
q = (( float((knots[i+p+1] - u))/float((knots[i+p+1] - knots[i+1])))
* N(u,i+1,p-1,knots))
except ZeroDivisionError:
q = 0.0
return float(k + q)
|
python
|
def N(u,i,p,knots):
"""Compute Spline Basis
Evaluates the spline basis of order p defined by knots
at knot i and point u.
"""
if p == 0:
if knots[i] < u and u <=knots[i+1]:
return 1.0
else:
return 0.0
else:
try:
k = (( float((u-knots[i]))/float((knots[i+p] - knots[i]) ))
* N(u,i,p-1,knots))
except ZeroDivisionError:
k = 0.0
try:
q = (( float((knots[i+p+1] - u))/float((knots[i+p+1] - knots[i+1])))
* N(u,i+1,p-1,knots))
except ZeroDivisionError:
q = 0.0
return float(k + q)
|
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Compute Spline Basis
Evaluates the spline basis of order p defined by knots
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|
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"and",
"point",
"u",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/spline_base.py#L322-L344
|
nwilming/ocupy
|
ocupy/measures.py
|
prediction_scores
|
def prediction_scores(prediction, fm, **kw):
"""
Evaluates a prediction against fixations in a fixmat with different measures.
The default measures which are used are AUC, NSS and KL-divergence. This
can be changed by setting the list of measures with set_scores.
As different measures need potentially different parameters, the kw
dictionary can be used to pass arguments to measures. Every named
argument (except fm and prediction) of a measure that is included in
kw.keys() will be filled with the value stored in kw.
Example:
>>> prediction_scores(P, FM, ctr_loc = (y,x))
In this case the AUC will be computed with control points (y,x), because
the measure 'roc_model' has 'ctr_loc' as named argument.
Input:
prediction : 2D numpy array
The prediction that should be evaluated
fm : Fixmat
The eyetracking data to evaluate against
Output:
Tuple of prediction scores. The order of the scores is determined
by order of measures.scores.
"""
if prediction == None:
return [np.NaN for measure in scores]
results = []
for measure in scores:
(args, _, _, _) = inspect.getargspec(measure)
if len(args)>2:
# Filter dictionary, such that only the keys that are
# expected by the measure are in it
mdict = {}
[mdict.update({key:value}) for (key, value) in list(kw.items())
if key in args]
score = measure(prediction, fm, **mdict)
else:
score = measure(prediction, fm)
results.append(score)
return results
|
python
|
def prediction_scores(prediction, fm, **kw):
"""
Evaluates a prediction against fixations in a fixmat with different measures.
The default measures which are used are AUC, NSS and KL-divergence. This
can be changed by setting the list of measures with set_scores.
As different measures need potentially different parameters, the kw
dictionary can be used to pass arguments to measures. Every named
argument (except fm and prediction) of a measure that is included in
kw.keys() will be filled with the value stored in kw.
Example:
>>> prediction_scores(P, FM, ctr_loc = (y,x))
In this case the AUC will be computed with control points (y,x), because
the measure 'roc_model' has 'ctr_loc' as named argument.
Input:
prediction : 2D numpy array
The prediction that should be evaluated
fm : Fixmat
The eyetracking data to evaluate against
Output:
Tuple of prediction scores. The order of the scores is determined
by order of measures.scores.
"""
if prediction == None:
return [np.NaN for measure in scores]
results = []
for measure in scores:
(args, _, _, _) = inspect.getargspec(measure)
if len(args)>2:
# Filter dictionary, such that only the keys that are
# expected by the measure are in it
mdict = {}
[mdict.update({key:value}) for (key, value) in list(kw.items())
if key in args]
score = measure(prediction, fm, **mdict)
else:
score = measure(prediction, fm)
results.append(score)
return results
|
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The default measures which are used are AUC, NSS and KL-divergence. This
can be changed by setting the list of measures with set_scores.
As different measures need potentially different parameters, the kw
dictionary can be used to pass arguments to measures. Every named
argument (except fm and prediction) of a measure that is included in
kw.keys() will be filled with the value stored in kw.
Example:
>>> prediction_scores(P, FM, ctr_loc = (y,x))
In this case the AUC will be computed with control points (y,x), because
the measure 'roc_model' has 'ctr_loc' as named argument.
Input:
prediction : 2D numpy array
The prediction that should be evaluated
fm : Fixmat
The eyetracking data to evaluate against
Output:
Tuple of prediction scores. The order of the scores is determined
by order of measures.scores.
|
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"in",
"a",
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"measures",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L23-L64
|
nwilming/ocupy
|
ocupy/measures.py
|
kldiv_model
|
def kldiv_model(prediction, fm):
"""
wraps kldiv functionality for model evaluation
input:
prediction: 2D matrix
the model salience map
fm : fixmat
Should be filtered for the image corresponding to the prediction
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
q = np.array(prediction, copy=True)
q -= np.min(q.flatten())
q /= np.sum(q.flatten())
return kldiv(None, q, distp = fm, scale_factor = r_x)
|
python
|
def kldiv_model(prediction, fm):
"""
wraps kldiv functionality for model evaluation
input:
prediction: 2D matrix
the model salience map
fm : fixmat
Should be filtered for the image corresponding to the prediction
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
q = np.array(prediction, copy=True)
q -= np.min(q.flatten())
q /= np.sum(q.flatten())
return kldiv(None, q, distp = fm, scale_factor = r_x)
|
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wraps kldiv functionality for model evaluation
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prediction: 2D matrix
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|
[
"wraps",
"kldiv",
"functionality",
"for",
"model",
"evaluation"
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L80-L94
|
nwilming/ocupy
|
ocupy/measures.py
|
kldiv
|
def kldiv(p, q, distp = None, distq = None, scale_factor = 1):
"""
Computes the Kullback-Leibler divergence between two distributions.
Parameters
p : Matrix
The first probability distribution
q : Matrix
The second probability distribution
distp : fixmat
If p is None, distp is used to compute a FDM which
is then taken as 1st probability distribution.
distq : fixmat
If q is None, distq is used to compute a FDM which is
then taken as 2dn probability distribution.
scale_factor : double
Determines the size of FDM computed from distq or distp.
"""
assert q != None or distq != None, "Either q or distq have to be given"
assert p != None or distp != None, "Either p or distp have to be given"
try:
if p == None:
p = compute_fdm(distp, scale_factor = scale_factor)
if q == None:
q = compute_fdm(distq, scale_factor = scale_factor)
except RuntimeError:
return np.NaN
q += np.finfo(q.dtype).eps
p += np.finfo(p.dtype).eps
kl = np.sum( p * (np.log2(p / q)))
return kl
|
python
|
def kldiv(p, q, distp = None, distq = None, scale_factor = 1):
"""
Computes the Kullback-Leibler divergence between two distributions.
Parameters
p : Matrix
The first probability distribution
q : Matrix
The second probability distribution
distp : fixmat
If p is None, distp is used to compute a FDM which
is then taken as 1st probability distribution.
distq : fixmat
If q is None, distq is used to compute a FDM which is
then taken as 2dn probability distribution.
scale_factor : double
Determines the size of FDM computed from distq or distp.
"""
assert q != None or distq != None, "Either q or distq have to be given"
assert p != None or distp != None, "Either p or distp have to be given"
try:
if p == None:
p = compute_fdm(distp, scale_factor = scale_factor)
if q == None:
q = compute_fdm(distq, scale_factor = scale_factor)
except RuntimeError:
return np.NaN
q += np.finfo(q.dtype).eps
p += np.finfo(p.dtype).eps
kl = np.sum( p * (np.log2(p / q)))
return kl
|
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Computes the Kullback-Leibler divergence between two distributions.
Parameters
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The first probability distribution
q : Matrix
The second probability distribution
distp : fixmat
If p is None, distp is used to compute a FDM which
is then taken as 1st probability distribution.
distq : fixmat
If q is None, distq is used to compute a FDM which is
then taken as 2dn probability distribution.
scale_factor : double
Determines the size of FDM computed from distq or distp.
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[
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L96-L129
|
nwilming/ocupy
|
ocupy/measures.py
|
kldiv_cs_model
|
def kldiv_cs_model(prediction, fm):
"""
Computes Chao-Shen corrected KL-divergence between prediction
and fdm made from fixations in fm.
Parameters :
prediction : np.ndarray
a fixation density map
fm : FixMat object
"""
# compute histogram of fixations needed for ChaoShen corrected kl-div
# image category must exist (>-1) and image_size must be non-empty
assert(len(fm.image_size) == 2 and (fm.image_size[0] > 0) and
(fm.image_size[1] > 0))
assert(-1 not in fm.category)
# check whether fixmat contains fixations
if len(fm.x) == 0:
return np.NaN
(scale_factor, _) = calc_resize_factor(prediction, fm.image_size)
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
e_y = np.arange(0, np.round(scale_factor*fm.image_size[0]+1))
e_x = np.arange(0, np.round(scale_factor*fm.image_size[1]+1))
samples = np.array(list(zip((scale_factor*fm.y), (scale_factor*fm.x))))
(fdm, _) = np.histogramdd(samples, (e_y, e_x))
# compute ChaoShen corrected kl-div
q = np.array(prediction, copy = True)
q[q == 0] = np.finfo(q.dtype).eps
q /= np.sum(q)
(H, pa, la) = chao_shen(fdm)
q = q[fdm > 0]
cross_entropy = -np.sum((pa * np.log2(q)) / la)
return (cross_entropy - H)
|
python
|
def kldiv_cs_model(prediction, fm):
"""
Computes Chao-Shen corrected KL-divergence between prediction
and fdm made from fixations in fm.
Parameters :
prediction : np.ndarray
a fixation density map
fm : FixMat object
"""
# compute histogram of fixations needed for ChaoShen corrected kl-div
# image category must exist (>-1) and image_size must be non-empty
assert(len(fm.image_size) == 2 and (fm.image_size[0] > 0) and
(fm.image_size[1] > 0))
assert(-1 not in fm.category)
# check whether fixmat contains fixations
if len(fm.x) == 0:
return np.NaN
(scale_factor, _) = calc_resize_factor(prediction, fm.image_size)
# this specifies left edges of the histogram bins, i.e. fixations between
# ]0 binedge[0]] are included. --> fixations are ceiled
e_y = np.arange(0, np.round(scale_factor*fm.image_size[0]+1))
e_x = np.arange(0, np.round(scale_factor*fm.image_size[1]+1))
samples = np.array(list(zip((scale_factor*fm.y), (scale_factor*fm.x))))
(fdm, _) = np.histogramdd(samples, (e_y, e_x))
# compute ChaoShen corrected kl-div
q = np.array(prediction, copy = True)
q[q == 0] = np.finfo(q.dtype).eps
q /= np.sum(q)
(H, pa, la) = chao_shen(fdm)
q = q[fdm > 0]
cross_entropy = -np.sum((pa * np.log2(q)) / la)
return (cross_entropy - H)
|
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fm : FixMat object
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L131-L164
|
nwilming/ocupy
|
ocupy/measures.py
|
chao_shen
|
def chao_shen(q):
"""
Computes some terms needed for the Chao-Shen KL correction.
"""
yx = q[q > 0] # remove bins with zero counts
n = np.sum(yx)
p = yx.astype(float)/n
f1 = np.sum(yx == 1) # number of singletons in the sample
if f1 == n: # avoid C == 0
f1 -= 1
C = 1 - (f1/n) # estimated coverage of the sample
pa = C * p # coverage adjusted empirical frequencies
la = (1 - (1 - pa) ** n) # probability to see a bin (species) in the sample
H = -np.sum((pa * np.log2(pa)) / la)
return (H, pa, la)
|
python
|
def chao_shen(q):
"""
Computes some terms needed for the Chao-Shen KL correction.
"""
yx = q[q > 0] # remove bins with zero counts
n = np.sum(yx)
p = yx.astype(float)/n
f1 = np.sum(yx == 1) # number of singletons in the sample
if f1 == n: # avoid C == 0
f1 -= 1
C = 1 - (f1/n) # estimated coverage of the sample
pa = C * p # coverage adjusted empirical frequencies
la = (1 - (1 - pa) ** n) # probability to see a bin (species) in the sample
H = -np.sum((pa * np.log2(pa)) / la)
return (H, pa, la)
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L167-L181
|
nwilming/ocupy
|
ocupy/measures.py
|
correlation_model
|
def correlation_model(prediction, fm):
"""
wraps numpy.corrcoef functionality for model evaluation
input:
prediction: 2D Matrix
the model salience map
fm: fixmat
Used to compute a FDM to which the prediction is compared.
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
fdm = compute_fdm(fm, scale_factor = r_x)
return np.corrcoef(fdm.flatten(), prediction.flatten())[0,1]
|
python
|
def correlation_model(prediction, fm):
"""
wraps numpy.corrcoef functionality for model evaluation
input:
prediction: 2D Matrix
the model salience map
fm: fixmat
Used to compute a FDM to which the prediction is compared.
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
fdm = compute_fdm(fm, scale_factor = r_x)
return np.corrcoef(fdm.flatten(), prediction.flatten())[0,1]
|
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wraps numpy.corrcoef functionality for model evaluation
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prediction: 2D Matrix
the model salience map
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Used to compute a FDM to which the prediction is compared.
|
[
"wraps",
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"functionality",
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"model",
"evaluation"
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L184-L196
|
nwilming/ocupy
|
ocupy/measures.py
|
nss_model
|
def nss_model(prediction, fm):
"""
wraps nss functionality for model evaluation
input:
prediction: 2D matrix
the model salience map
fm : fixmat
Fixations that define the actuals
"""
(r_y, r_x) = calc_resize_factor(prediction, fm.image_size)
fix = ((np.array(fm.y-1)*r_y).astype(int),
(np.array(fm.x-1)*r_x).astype(int))
return nss(prediction, fix)
|
python
|
def nss_model(prediction, fm):
"""
wraps nss functionality for model evaluation
input:
prediction: 2D matrix
the model salience map
fm : fixmat
Fixations that define the actuals
"""
(r_y, r_x) = calc_resize_factor(prediction, fm.image_size)
fix = ((np.array(fm.y-1)*r_y).astype(int),
(np.array(fm.x-1)*r_x).astype(int))
return nss(prediction, fix)
|
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wraps nss functionality for model evaluation
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the model salience map
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|
[
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"functionality",
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L199-L212
|
nwilming/ocupy
|
ocupy/measures.py
|
nss
|
def nss(prediction, fix):
"""
Compute the normalized scanpath salience
input:
fix : list, l[0] contains y, l[1] contains x
"""
prediction = prediction - np.mean(prediction)
prediction = prediction / np.std(prediction)
return np.mean(prediction[fix[0], fix[1]])
|
python
|
def nss(prediction, fix):
"""
Compute the normalized scanpath salience
input:
fix : list, l[0] contains y, l[1] contains x
"""
prediction = prediction - np.mean(prediction)
prediction = prediction / np.std(prediction)
return np.mean(prediction[fix[0], fix[1]])
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[
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L215-L225
|
nwilming/ocupy
|
ocupy/measures.py
|
roc_model
|
def roc_model(prediction, fm, ctr_loc = None, ctr_size = None):
"""
wraps roc functionality for model evaluation
Parameters:
prediction: 2D array
the model salience map
fm : fixmat
Fixations that define locations of the actuals
ctr_loc : tuple of (y.x) coordinates, optional
Allows to specify control points for spatial
bias correction
ctr_size : two element tuple, optional
Specifies the assumed image size of the control locations,
defaults to fm.image_size
"""
# check if prediction is a valid numpy array
assert type(prediction) == np.ndarray
# check whether scaling preserved aspect ratio
(r_y, r_x) = calc_resize_factor(prediction, fm.image_size)
# read out values in the fdm at actual fixation locations
# .astype(int) floors numbers in np.array
y_index = (r_y * np.array(fm.y-1)).astype(int)
x_index = (r_x * np.array(fm.x-1)).astype(int)
actuals = prediction[y_index, x_index]
if not ctr_loc:
xc = np.random.randint(0, prediction.shape[1], 1000)
yc = np.random.randint(0, prediction.shape[0], 1000)
ctr_loc = (yc.astype(int), xc.astype(int))
else:
if not ctr_size:
ctr_size = fm.image_size
else:
(r_y, r_x) = calc_resize_factor(prediction, ctr_size)
ctr_loc = ((r_y * np.array(ctr_loc[0])).astype(int),
(r_x * np.array(ctr_loc[1])).astype(int))
controls = prediction[ctr_loc[0], ctr_loc[1]]
return fast_roc(actuals, controls)[0]
|
python
|
def roc_model(prediction, fm, ctr_loc = None, ctr_size = None):
"""
wraps roc functionality for model evaluation
Parameters:
prediction: 2D array
the model salience map
fm : fixmat
Fixations that define locations of the actuals
ctr_loc : tuple of (y.x) coordinates, optional
Allows to specify control points for spatial
bias correction
ctr_size : two element tuple, optional
Specifies the assumed image size of the control locations,
defaults to fm.image_size
"""
# check if prediction is a valid numpy array
assert type(prediction) == np.ndarray
# check whether scaling preserved aspect ratio
(r_y, r_x) = calc_resize_factor(prediction, fm.image_size)
# read out values in the fdm at actual fixation locations
# .astype(int) floors numbers in np.array
y_index = (r_y * np.array(fm.y-1)).astype(int)
x_index = (r_x * np.array(fm.x-1)).astype(int)
actuals = prediction[y_index, x_index]
if not ctr_loc:
xc = np.random.randint(0, prediction.shape[1], 1000)
yc = np.random.randint(0, prediction.shape[0], 1000)
ctr_loc = (yc.astype(int), xc.astype(int))
else:
if not ctr_size:
ctr_size = fm.image_size
else:
(r_y, r_x) = calc_resize_factor(prediction, ctr_size)
ctr_loc = ((r_y * np.array(ctr_loc[0])).astype(int),
(r_x * np.array(ctr_loc[1])).astype(int))
controls = prediction[ctr_loc[0], ctr_loc[1]]
return fast_roc(actuals, controls)[0]
|
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wraps roc functionality for model evaluation
Parameters:
prediction: 2D array
the model salience map
fm : fixmat
Fixations that define locations of the actuals
ctr_loc : tuple of (y.x) coordinates, optional
Allows to specify control points for spatial
bias correction
ctr_size : two element tuple, optional
Specifies the assumed image size of the control locations,
defaults to fm.image_size
|
[
"wraps",
"roc",
"functionality",
"for",
"model",
"evaluation"
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L228-L266
|
nwilming/ocupy
|
ocupy/measures.py
|
fast_roc
|
def fast_roc(actuals, controls):
"""
approximates the area under the roc curve for sets of actuals and controls.
Uses all values appearing in actuals as thresholds and lower sum
interpolation. Also returns arrays of the true positive rate and the false
positive rate that can be used for plotting the roc curve.
Parameters:
actuals : list
A list of numeric values for positive observations.
controls : list
A list of numeric values for negative observations.
"""
assert(type(actuals) is np.ndarray)
assert(type(controls) is np.ndarray)
actuals = np.ravel(actuals)
controls = np.ravel(controls)
if np.isnan(actuals).any():
raise RuntimeError('NaN found in actuals')
if np.isnan(controls).any():
raise RuntimeError('NaN found in controls')
thresholds = np.hstack([-np.inf, np.unique(actuals), np.inf])[::-1]
true_pos_rate = np.empty(thresholds.size)
false_pos_rate = np.empty(thresholds.size)
num_act = float(len(actuals))
num_ctr = float(len(controls))
for i, value in enumerate(thresholds):
true_pos_rate[i] = (actuals >= value).sum() / num_act
false_pos_rate[i] = (controls >= value).sum() / num_ctr
auc = np.dot(np.diff(false_pos_rate), true_pos_rate[0:-1])
# treat cases where TPR of one is not reached before FPR of one
# by using trapezoidal integration for the last segment
# (add the missing triangle)
if false_pos_rate[-2] == 1:
auc += ((1-true_pos_rate[-3])*.5*(1-false_pos_rate[-3]))
return (auc, true_pos_rate, false_pos_rate)
|
python
|
def fast_roc(actuals, controls):
"""
approximates the area under the roc curve for sets of actuals and controls.
Uses all values appearing in actuals as thresholds and lower sum
interpolation. Also returns arrays of the true positive rate and the false
positive rate that can be used for plotting the roc curve.
Parameters:
actuals : list
A list of numeric values for positive observations.
controls : list
A list of numeric values for negative observations.
"""
assert(type(actuals) is np.ndarray)
assert(type(controls) is np.ndarray)
actuals = np.ravel(actuals)
controls = np.ravel(controls)
if np.isnan(actuals).any():
raise RuntimeError('NaN found in actuals')
if np.isnan(controls).any():
raise RuntimeError('NaN found in controls')
thresholds = np.hstack([-np.inf, np.unique(actuals), np.inf])[::-1]
true_pos_rate = np.empty(thresholds.size)
false_pos_rate = np.empty(thresholds.size)
num_act = float(len(actuals))
num_ctr = float(len(controls))
for i, value in enumerate(thresholds):
true_pos_rate[i] = (actuals >= value).sum() / num_act
false_pos_rate[i] = (controls >= value).sum() / num_ctr
auc = np.dot(np.diff(false_pos_rate), true_pos_rate[0:-1])
# treat cases where TPR of one is not reached before FPR of one
# by using trapezoidal integration for the last segment
# (add the missing triangle)
if false_pos_rate[-2] == 1:
auc += ((1-true_pos_rate[-3])*.5*(1-false_pos_rate[-3]))
return (auc, true_pos_rate, false_pos_rate)
|
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approximates the area under the roc curve for sets of actuals and controls.
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interpolation. Also returns arrays of the true positive rate and the false
positive rate that can be used for plotting the roc curve.
Parameters:
actuals : list
A list of numeric values for positive observations.
controls : list
A list of numeric values for negative observations.
|
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L269-L307
|
nwilming/ocupy
|
ocupy/measures.py
|
faster_roc
|
def faster_roc(actuals, controls):
"""
Histogram based implementation of AUC unde ROC curve.
Parameters:
actuals : list
A list of numeric values for positive observations.
controls : list
A list of numeric values for negative observations.
"""
assert(type(actuals) is np.ndarray)
assert(type(controls) is np.ndarray)
if len(actuals)<500:
raise RuntimeError('This method might be incorrect when '+
'not enough actuals are present. Needs to be checked before '+
'proceeding. Stopping here for you to do so.')
actuals = np.ravel(actuals)
controls = np.ravel(controls)
if np.isnan(actuals).any():
raise RuntimeError('NaN found in actuals')
if np.isnan(controls).any():
raise RuntimeError('NaN found in controls')
thresholds = np.hstack([-np.inf, np.unique(actuals), np.inf])+np.finfo(float).eps
true_pos_rate = np.nan*np.empty(thresholds.size-1)
false_pos_rate = np.nan*np.empty(thresholds.size-1)
num_act = float(len(actuals))
num_ctr = float(len(controls))
actuals = 1-(np.cumsum(np.histogram(actuals, thresholds)[0])/num_act)
controls = 1-(np.cumsum(np.histogram(controls, thresholds)[0])/num_ctr)
true_pos_rate = actuals
false_pos_rate = controls
#true_pos_rate = np.concatenate(([0], true_pos_rate, [1]))
false_pos_rate = false_pos_rate
auc = -1*np.dot(np.diff(false_pos_rate), true_pos_rate[0:-1])
# treat cases where TPR of one is not reached before FPR of one
# by using trapezoidal integration for the last segment
# (add the missing triangle)
if false_pos_rate[-2] == 1:
auc += ((1-true_pos_rate[-3])*.5*(1-false_pos_rate[-3]))
return (auc, true_pos_rate, false_pos_rate)
|
python
|
def faster_roc(actuals, controls):
"""
Histogram based implementation of AUC unde ROC curve.
Parameters:
actuals : list
A list of numeric values for positive observations.
controls : list
A list of numeric values for negative observations.
"""
assert(type(actuals) is np.ndarray)
assert(type(controls) is np.ndarray)
if len(actuals)<500:
raise RuntimeError('This method might be incorrect when '+
'not enough actuals are present. Needs to be checked before '+
'proceeding. Stopping here for you to do so.')
actuals = np.ravel(actuals)
controls = np.ravel(controls)
if np.isnan(actuals).any():
raise RuntimeError('NaN found in actuals')
if np.isnan(controls).any():
raise RuntimeError('NaN found in controls')
thresholds = np.hstack([-np.inf, np.unique(actuals), np.inf])+np.finfo(float).eps
true_pos_rate = np.nan*np.empty(thresholds.size-1)
false_pos_rate = np.nan*np.empty(thresholds.size-1)
num_act = float(len(actuals))
num_ctr = float(len(controls))
actuals = 1-(np.cumsum(np.histogram(actuals, thresholds)[0])/num_act)
controls = 1-(np.cumsum(np.histogram(controls, thresholds)[0])/num_ctr)
true_pos_rate = actuals
false_pos_rate = controls
#true_pos_rate = np.concatenate(([0], true_pos_rate, [1]))
false_pos_rate = false_pos_rate
auc = -1*np.dot(np.diff(false_pos_rate), true_pos_rate[0:-1])
# treat cases where TPR of one is not reached before FPR of one
# by using trapezoidal integration for the last segment
# (add the missing triangle)
if false_pos_rate[-2] == 1:
auc += ((1-true_pos_rate[-3])*.5*(1-false_pos_rate[-3]))
return (auc, true_pos_rate, false_pos_rate)
|
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controls : list
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L309-L351
|
nwilming/ocupy
|
ocupy/measures.py
|
emd_model
|
def emd_model(prediction, fm):
"""
wraps emd functionality for model evaluation
requires:
OpenCV python bindings
input:
prediction: the model salience map
fm : fixmat filtered for the image corresponding to the prediction
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
gt = fixmat.compute_fdm(fm, scale_factor = r_x)
return emd(prediction, gt)
|
python
|
def emd_model(prediction, fm):
"""
wraps emd functionality for model evaluation
requires:
OpenCV python bindings
input:
prediction: the model salience map
fm : fixmat filtered for the image corresponding to the prediction
"""
(_, r_x) = calc_resize_factor(prediction, fm.image_size)
gt = fixmat.compute_fdm(fm, scale_factor = r_x)
return emd(prediction, gt)
|
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|
[
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train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L382-L395
|
nwilming/ocupy
|
ocupy/measures.py
|
emd
|
def emd(prediction, ground_truth):
"""
Compute the Eart Movers Distance between prediction and model.
This implementation uses opencv for doing the actual work.
Unfortunately, at the time of implementation only the SWIG
bindings werer available and the numpy arrays have to
converted by hand. This changes with opencv 2.1. """
import opencv
if not (prediction.shape == ground_truth.shape):
raise RuntimeError('Shapes of prediction and ground truth have' +
' to be equal. They are: %s, %s'
%(str(prediction.shape), str(ground_truth.shape)))
(x, y) = np.meshgrid(list(range(0, prediction.shape[1])),
list(range(0, prediction.shape[0])))
s1 = np.array([x.flatten(), y.flatten(), prediction.flatten()]).T
s2 = np.array([x.flatten(), y.flatten(), ground_truth.flatten()]).T
s1m = opencv.cvCreateMat(s1.shape[0], s2.shape[1], opencv.CV_32FC1)
s2m = opencv.cvCreateMat(s1.shape[0], s2.shape[1], opencv.CV_32FC1)
for r in range(0, s1.shape[0]):
for c in range(0, s1.shape[1]):
s1m[r, c] = float(s1[r, c])
s2m[r, c] = float(s2[r, c])
d = opencv.cvCalcEMD2(s1m, s2m, opencv.CV_DIST_L2)
return d
|
python
|
def emd(prediction, ground_truth):
"""
Compute the Eart Movers Distance between prediction and model.
This implementation uses opencv for doing the actual work.
Unfortunately, at the time of implementation only the SWIG
bindings werer available and the numpy arrays have to
converted by hand. This changes with opencv 2.1. """
import opencv
if not (prediction.shape == ground_truth.shape):
raise RuntimeError('Shapes of prediction and ground truth have' +
' to be equal. They are: %s, %s'
%(str(prediction.shape), str(ground_truth.shape)))
(x, y) = np.meshgrid(list(range(0, prediction.shape[1])),
list(range(0, prediction.shape[0])))
s1 = np.array([x.flatten(), y.flatten(), prediction.flatten()]).T
s2 = np.array([x.flatten(), y.flatten(), ground_truth.flatten()]).T
s1m = opencv.cvCreateMat(s1.shape[0], s2.shape[1], opencv.CV_32FC1)
s2m = opencv.cvCreateMat(s1.shape[0], s2.shape[1], opencv.CV_32FC1)
for r in range(0, s1.shape[0]):
for c in range(0, s1.shape[1]):
s1m[r, c] = float(s1[r, c])
s2m[r, c] = float(s2[r, c])
d = opencv.cvCalcEMD2(s1m, s2m, opencv.CV_DIST_L2)
return d
|
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Compute the Eart Movers Distance between prediction and model.
This implementation uses opencv for doing the actual work.
Unfortunately, at the time of implementation only the SWIG
bindings werer available and the numpy arrays have to
converted by hand. This changes with opencv 2.1.
|
[
"Compute",
"the",
"Eart",
"Movers",
"Distance",
"between",
"prediction",
"and",
"model",
"."
] |
train
|
https://github.com/nwilming/ocupy/blob/a0bd64f822576feaa502939d6bafd1183b237d16/ocupy/measures.py#L398-L423
|
kurtmckee/listparser
|
listparser/dates.py
|
_rfc822
|
def _rfc822(date):
"""Parse RFC 822 dates and times
http://tools.ietf.org/html/rfc822#section-5
There are some formatting differences that are accounted for:
1. Years may be two or four digits.
2. The month and day can be swapped.
3. Additional timezone names are supported.
4. A default time and timezone are assumed if only a date is present.
5.
"""
daynames = set(['mon', 'tue', 'wed', 'thu', 'fri', 'sat', 'sun'])
months = {
'jan': 1, 'feb': 2, 'mar': 3, 'apr': 4, 'may': 5, 'jun': 6,
'jul': 7, 'aug': 8, 'sep': 9, 'oct': 10, 'nov': 11, 'dec': 12,
}
timezonenames = {
'ut': 0, 'gmt': 0, 'z': 0,
'adt': -3, 'ast': -4, 'at': -4,
'edt': -4, 'est': -5, 'et': -5,
'cdt': -5, 'cst': -6, 'ct': -6,
'mdt': -6, 'mst': -7, 'mt': -7,
'pdt': -7, 'pst': -8, 'pt': -8,
'a': -1, 'n': 1,
'm': -12, 'y': 12,
}
parts = date.lower().split()
if len(parts) < 5:
# Assume that the time and timezone are missing
parts.extend(('00:00:00', '0000'))
# Remove the day name
if parts[0][:3] in daynames:
parts = parts[1:]
if len(parts) < 5:
# If there are still fewer than five parts, there's not enough
# information to interpret this
return None
try:
day = int(parts[0])
except ValueError:
# Check if the day and month are swapped
if months.get(parts[0][:3]):
try:
day = int(parts[1])
except ValueError:
return None
else:
parts[1] = parts[0]
else:
return None
month = months.get(parts[1][:3])
if not month:
return None
try:
year = int(parts[2])
except ValueError:
return None
# Normalize two-digit years:
# Anything in the 90's is interpreted as 1990 and on
# Anything 89 or less is interpreted as 2089 or before
if len(parts[2]) <= 2:
year += (1900, 2000)[year < 90]
timeparts = parts[3].split(':')
timeparts = timeparts + ([0] * (3 - len(timeparts)))
try:
(hour, minute, second) = map(int, timeparts)
except ValueError:
return None
tzhour = 0
tzmin = 0
# Strip 'Etc/' from the timezone
if parts[4].startswith('etc/'):
parts[4] = parts[4][4:]
# Normalize timezones that start with 'gmt':
# GMT-05:00 => -0500
# GMT => GMT
if parts[4].startswith('gmt'):
parts[4] = ''.join(parts[4][3:].split(':')) or 'gmt'
# Handle timezones like '-0500', '+0500', and 'EST'
if parts[4] and parts[4][0] in ('-', '+'):
try:
tzhour = int(parts[4][1:3])
tzmin = int(parts[4][3:])
except ValueError:
return None
if parts[4].startswith('-'):
tzhour = tzhour * -1
tzmin = tzmin * -1
else:
tzhour = timezonenames.get(parts[4], 0)
# Create the datetime object and timezone delta objects
try:
stamp = datetime.datetime(year, month, day, hour, minute, second)
except ValueError:
return None
delta = datetime.timedelta(0, 0, 0, 0, tzmin, tzhour)
# Return the date and timestamp in a UTC 9-tuple
try:
return stamp - delta
except OverflowError:
return None
|
python
|
def _rfc822(date):
"""Parse RFC 822 dates and times
http://tools.ietf.org/html/rfc822#section-5
There are some formatting differences that are accounted for:
1. Years may be two or four digits.
2. The month and day can be swapped.
3. Additional timezone names are supported.
4. A default time and timezone are assumed if only a date is present.
5.
"""
daynames = set(['mon', 'tue', 'wed', 'thu', 'fri', 'sat', 'sun'])
months = {
'jan': 1, 'feb': 2, 'mar': 3, 'apr': 4, 'may': 5, 'jun': 6,
'jul': 7, 'aug': 8, 'sep': 9, 'oct': 10, 'nov': 11, 'dec': 12,
}
timezonenames = {
'ut': 0, 'gmt': 0, 'z': 0,
'adt': -3, 'ast': -4, 'at': -4,
'edt': -4, 'est': -5, 'et': -5,
'cdt': -5, 'cst': -6, 'ct': -6,
'mdt': -6, 'mst': -7, 'mt': -7,
'pdt': -7, 'pst': -8, 'pt': -8,
'a': -1, 'n': 1,
'm': -12, 'y': 12,
}
parts = date.lower().split()
if len(parts) < 5:
# Assume that the time and timezone are missing
parts.extend(('00:00:00', '0000'))
# Remove the day name
if parts[0][:3] in daynames:
parts = parts[1:]
if len(parts) < 5:
# If there are still fewer than five parts, there's not enough
# information to interpret this
return None
try:
day = int(parts[0])
except ValueError:
# Check if the day and month are swapped
if months.get(parts[0][:3]):
try:
day = int(parts[1])
except ValueError:
return None
else:
parts[1] = parts[0]
else:
return None
month = months.get(parts[1][:3])
if not month:
return None
try:
year = int(parts[2])
except ValueError:
return None
# Normalize two-digit years:
# Anything in the 90's is interpreted as 1990 and on
# Anything 89 or less is interpreted as 2089 or before
if len(parts[2]) <= 2:
year += (1900, 2000)[year < 90]
timeparts = parts[3].split(':')
timeparts = timeparts + ([0] * (3 - len(timeparts)))
try:
(hour, minute, second) = map(int, timeparts)
except ValueError:
return None
tzhour = 0
tzmin = 0
# Strip 'Etc/' from the timezone
if parts[4].startswith('etc/'):
parts[4] = parts[4][4:]
# Normalize timezones that start with 'gmt':
# GMT-05:00 => -0500
# GMT => GMT
if parts[4].startswith('gmt'):
parts[4] = ''.join(parts[4][3:].split(':')) or 'gmt'
# Handle timezones like '-0500', '+0500', and 'EST'
if parts[4] and parts[4][0] in ('-', '+'):
try:
tzhour = int(parts[4][1:3])
tzmin = int(parts[4][3:])
except ValueError:
return None
if parts[4].startswith('-'):
tzhour = tzhour * -1
tzmin = tzmin * -1
else:
tzhour = timezonenames.get(parts[4], 0)
# Create the datetime object and timezone delta objects
try:
stamp = datetime.datetime(year, month, day, hour, minute, second)
except ValueError:
return None
delta = datetime.timedelta(0, 0, 0, 0, tzmin, tzhour)
# Return the date and timestamp in a UTC 9-tuple
try:
return stamp - delta
except OverflowError:
return None
|
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http://tools.ietf.org/html/rfc822#section-5
There are some formatting differences that are accounted for:
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2. The month and day can be swapped.
3. Additional timezone names are supported.
4. A default time and timezone are assumed if only a date is present.
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|
[
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train
|
https://github.com/kurtmckee/listparser/blob/f9bc310a0ce567cd0611fea68be99974021f53c7/listparser/dates.py#L25-L126
|
kurtmckee/listparser
|
listparser/dates.py
|
_to_rfc822
|
def _to_rfc822(date):
"""_to_rfc822(datetime.datetime) -> str
The datetime `strftime` method is subject to locale-specific
day and month names, so this function hardcodes the conversion."""
months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun',
'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']
days = ['Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat', 'Sun']
fmt = '{day}, {d:02} {month} {y:04} {h:02}:{m:02}:{s:02} GMT'
return fmt.format(
day=days[date.weekday()],
d=date.day,
month=months[date.month - 1],
y=date.year,
h=date.hour,
m=date.minute,
s=date.second,
)
|
python
|
def _to_rfc822(date):
"""_to_rfc822(datetime.datetime) -> str
The datetime `strftime` method is subject to locale-specific
day and month names, so this function hardcodes the conversion."""
months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun',
'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']
days = ['Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat', 'Sun']
fmt = '{day}, {d:02} {month} {y:04} {h:02}:{m:02}:{s:02} GMT'
return fmt.format(
day=days[date.weekday()],
d=date.day,
month=months[date.month - 1],
y=date.year,
h=date.hour,
m=date.minute,
s=date.second,
)
|
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_to_rfc822(datetime.datetime) -> str
The datetime `strftime` method is subject to locale-specific
day and month names, so this function hardcodes the conversion.
|
[
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train
|
https://github.com/kurtmckee/listparser/blob/f9bc310a0ce567cd0611fea68be99974021f53c7/listparser/dates.py#L129-L145
|
cpburnz/python-sql-parameters
|
sqlparams/__init__.py
|
SQLParams.format
|
def format(self, sql, params):
"""
Formats the SQL query to use ordinal parameters instead of named
parameters.
*sql* (|string|) is the SQL query.
*params* (|dict|) maps each named parameter (|string|) to value
(|object|). If |self.named| is "numeric", then *params* can be
simply a |sequence| of values mapped by index.
Returns a 2-|tuple| containing: the formatted SQL query (|string|),
and the ordinal parameters (|list|).
"""
if isinstance(sql, unicode):
string_type = unicode
elif isinstance(sql, bytes):
string_type = bytes
sql = sql.decode(_BYTES_ENCODING)
else:
raise TypeError("sql:{!r} is not a unicode or byte string.".format(sql))
if self.named == 'numeric':
if isinstance(params, collections.Mapping):
params = {string_type(idx): val for idx, val in iteritems(params)}
elif isinstance(params, collections.Sequence) and not isinstance(params, (unicode, bytes)):
params = {string_type(idx): val for idx, val in enumerate(params, 1)}
if not isinstance(params, collections.Mapping):
raise TypeError("params:{!r} is not a dict.".format(params))
# Find named parameters.
names = self.match.findall(sql)
# Map named parameters to ordinals.
ord_params = []
name_to_ords = {}
for name in names:
value = params[name]
if isinstance(value, tuple):
ord_params.extend(value)
if name not in name_to_ords:
name_to_ords[name] = '(' + ','.join((self.replace,) * len(value)) + ')'
else:
ord_params.append(value)
if name not in name_to_ords:
name_to_ords[name] = self.replace
# Replace named parameters with ordinals.
sql = self.match.sub(lambda m: name_to_ords[m.group(1)], sql)
# Make sure the query is returned as the proper string type.
if string_type is bytes:
sql = sql.encode(_BYTES_ENCODING)
# Return formatted SQL and new ordinal parameters.
return sql, ord_params
|
python
|
def format(self, sql, params):
"""
Formats the SQL query to use ordinal parameters instead of named
parameters.
*sql* (|string|) is the SQL query.
*params* (|dict|) maps each named parameter (|string|) to value
(|object|). If |self.named| is "numeric", then *params* can be
simply a |sequence| of values mapped by index.
Returns a 2-|tuple| containing: the formatted SQL query (|string|),
and the ordinal parameters (|list|).
"""
if isinstance(sql, unicode):
string_type = unicode
elif isinstance(sql, bytes):
string_type = bytes
sql = sql.decode(_BYTES_ENCODING)
else:
raise TypeError("sql:{!r} is not a unicode or byte string.".format(sql))
if self.named == 'numeric':
if isinstance(params, collections.Mapping):
params = {string_type(idx): val for idx, val in iteritems(params)}
elif isinstance(params, collections.Sequence) and not isinstance(params, (unicode, bytes)):
params = {string_type(idx): val for idx, val in enumerate(params, 1)}
if not isinstance(params, collections.Mapping):
raise TypeError("params:{!r} is not a dict.".format(params))
# Find named parameters.
names = self.match.findall(sql)
# Map named parameters to ordinals.
ord_params = []
name_to_ords = {}
for name in names:
value = params[name]
if isinstance(value, tuple):
ord_params.extend(value)
if name not in name_to_ords:
name_to_ords[name] = '(' + ','.join((self.replace,) * len(value)) + ')'
else:
ord_params.append(value)
if name not in name_to_ords:
name_to_ords[name] = self.replace
# Replace named parameters with ordinals.
sql = self.match.sub(lambda m: name_to_ords[m.group(1)], sql)
# Make sure the query is returned as the proper string type.
if string_type is bytes:
sql = sql.encode(_BYTES_ENCODING)
# Return formatted SQL and new ordinal parameters.
return sql, ord_params
|
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train
|
https://github.com/cpburnz/python-sql-parameters/blob/828088a54b84aa904ec54c50af60f8aecc62a5f4/sqlparams/__init__.py#L245-L301
|
cpburnz/python-sql-parameters
|
sqlparams/__init__.py
|
SQLParams.formatmany
|
def formatmany(self, sql, many_params):
"""
Formats the SQL query to use ordinal parameters instead of named
parameters.
*sql* (|string|) is the SQL query.
*many_params* (|iterable|) contains each *params* to format.
- *params* (|dict|) maps each named parameter (|string|) to value
(|object|). If |self.named| is "numeric", then *params* can be
simply a |sequence| of values mapped by index.
Returns a 2-|tuple| containing: the formatted SQL query (|string|),
and a |list| containing each ordinal parameters (|list|).
"""
if isinstance(sql, unicode):
string_type = unicode
elif isinstance(sql, bytes):
string_type = bytes
sql = sql.decode(_BYTES_ENCODING)
else:
raise TypeError("sql:{!r} is not a unicode or byte string.".format(sql))
if not isinstance(many_params, collections.Iterable) or isinstance(many_params, (unicode, bytes)):
raise TypeError("many_params:{!r} is not iterable.".format(many_params))
# Find named parameters.
names = self.match.findall(sql)
name_set = set(names)
# Map named parameters to ordinals.
many_ord_params = []
name_to_ords = {}
name_to_len = {}
repl_str = self.replace
repl_tuple = (repl_str,)
for i, params in enumerate(many_params):
if self.named == 'numeric':
if isinstance(params, collections.Mapping):
params = {string_type(idx): val for idx, val in iteritems(params)}
elif isinstance(params, collections.Sequence) and not isinstance(params, (unicode, bytes)):
params = {string_type(idx): val for idx, val in enumerate(params, 1)}
if not isinstance(params, collections.Mapping):
raise TypeError("many_params[{}]:{!r} is not a dict.".format(i, params))
if not i: # first
# Map names to ordinals, and determine what names are tuples and
# what their lengths are.
for name in name_set:
value = params[name]
if isinstance(value, tuple):
tuple_len = len(value)
name_to_ords[name] = '(' + ','.join(repl_tuple * tuple_len) + ')'
name_to_len[name] = tuple_len
else:
name_to_ords[name] = repl_str
name_to_len[name] = None
# Make sure tuples match up and collapse tuples into ordinals.
ord_params = []
for name in names:
value = params[name]
tuple_len = name_to_len[name]
if tuple_len is not None:
if not isinstance(value, tuple):
raise TypeError("many_params[{}][{!r}]:{!r} was expected to be a tuple.".format(i, name, value))
elif len(value) != tuple_len:
raise ValueError("many_params[{}][{!r}]:{!r} length was expected to be {}.".format(i, name, value, tuple_len))
ord_params.extend(value)
else:
ord_params.append(value)
many_ord_params.append(ord_params)
# Replace named parameters with ordinals.
sql = self.match.sub(lambda m: name_to_ords[m.group(1)], sql)
# Make sure the query is returned as the proper string type.
if string_type is bytes:
sql = sql.encode(_BYTES_ENCODING)
# Return formatted SQL and new ordinal parameters.
return sql, many_ord_params
|
python
|
def formatmany(self, sql, many_params):
"""
Formats the SQL query to use ordinal parameters instead of named
parameters.
*sql* (|string|) is the SQL query.
*many_params* (|iterable|) contains each *params* to format.
- *params* (|dict|) maps each named parameter (|string|) to value
(|object|). If |self.named| is "numeric", then *params* can be
simply a |sequence| of values mapped by index.
Returns a 2-|tuple| containing: the formatted SQL query (|string|),
and a |list| containing each ordinal parameters (|list|).
"""
if isinstance(sql, unicode):
string_type = unicode
elif isinstance(sql, bytes):
string_type = bytes
sql = sql.decode(_BYTES_ENCODING)
else:
raise TypeError("sql:{!r} is not a unicode or byte string.".format(sql))
if not isinstance(many_params, collections.Iterable) or isinstance(many_params, (unicode, bytes)):
raise TypeError("many_params:{!r} is not iterable.".format(many_params))
# Find named parameters.
names = self.match.findall(sql)
name_set = set(names)
# Map named parameters to ordinals.
many_ord_params = []
name_to_ords = {}
name_to_len = {}
repl_str = self.replace
repl_tuple = (repl_str,)
for i, params in enumerate(many_params):
if self.named == 'numeric':
if isinstance(params, collections.Mapping):
params = {string_type(idx): val for idx, val in iteritems(params)}
elif isinstance(params, collections.Sequence) and not isinstance(params, (unicode, bytes)):
params = {string_type(idx): val for idx, val in enumerate(params, 1)}
if not isinstance(params, collections.Mapping):
raise TypeError("many_params[{}]:{!r} is not a dict.".format(i, params))
if not i: # first
# Map names to ordinals, and determine what names are tuples and
# what their lengths are.
for name in name_set:
value = params[name]
if isinstance(value, tuple):
tuple_len = len(value)
name_to_ords[name] = '(' + ','.join(repl_tuple * tuple_len) + ')'
name_to_len[name] = tuple_len
else:
name_to_ords[name] = repl_str
name_to_len[name] = None
# Make sure tuples match up and collapse tuples into ordinals.
ord_params = []
for name in names:
value = params[name]
tuple_len = name_to_len[name]
if tuple_len is not None:
if not isinstance(value, tuple):
raise TypeError("many_params[{}][{!r}]:{!r} was expected to be a tuple.".format(i, name, value))
elif len(value) != tuple_len:
raise ValueError("many_params[{}][{!r}]:{!r} length was expected to be {}.".format(i, name, value, tuple_len))
ord_params.extend(value)
else:
ord_params.append(value)
many_ord_params.append(ord_params)
# Replace named parameters with ordinals.
sql = self.match.sub(lambda m: name_to_ords[m.group(1)], sql)
# Make sure the query is returned as the proper string type.
if string_type is bytes:
sql = sql.encode(_BYTES_ENCODING)
# Return formatted SQL and new ordinal parameters.
return sql, many_ord_params
|
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|
[
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] |
train
|
https://github.com/cpburnz/python-sql-parameters/blob/828088a54b84aa904ec54c50af60f8aecc62a5f4/sqlparams/__init__.py#L303-L386
|
hecrj/reticular
|
reticular.py
|
_get_parser
|
def _get_parser(f):
"""
Gets the parser for the command f, if it not exists it creates a new one
"""
_COMMAND_GROUPS[f.__module__].load()
if f.__name__ not in _COMMAND_GROUPS[f.__module__].parsers:
parser = _COMMAND_GROUPS[f.__module__].parser_generator.add_parser(f.__name__, help=f.__doc__,
description=f.__doc__)
parser.set_defaults(func=f)
_COMMAND_GROUPS[f.__module__].parsers[f.__name__] = parser
return _COMMAND_GROUPS[f.__module__].parsers[f.__name__]
|
python
|
def _get_parser(f):
"""
Gets the parser for the command f, if it not exists it creates a new one
"""
_COMMAND_GROUPS[f.__module__].load()
if f.__name__ not in _COMMAND_GROUPS[f.__module__].parsers:
parser = _COMMAND_GROUPS[f.__module__].parser_generator.add_parser(f.__name__, help=f.__doc__,
description=f.__doc__)
parser.set_defaults(func=f)
_COMMAND_GROUPS[f.__module__].parsers[f.__name__] = parser
return _COMMAND_GROUPS[f.__module__].parsers[f.__name__]
|
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Gets the parser for the command f, if it not exists it creates a new one
|
[
"Gets",
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] |
train
|
https://github.com/hecrj/reticular/blob/b83c632459b3215284124373931fcaef76bc64e8/reticular.py#L180-L193
|
bear/ronkyuu
|
ronkyuu/webmention.py
|
findMentions
|
def findMentions(sourceURL, targetURL=None, exclude_domains=[], content=None, test_urls=True, headers={}, timeout=None):
"""Find all <a /> elements in the given html for a post. Only scan html element matching all criteria in look_in.
optionally the content to be scanned can be given as an argument.
If any have an href attribute that is not from the
one of the items in exclude_domains, append it to our lists.
:param sourceURL: the URL for the post we are scanning
:param exclude_domains: a list of domains to exclude from the search
:type exclude_domains: list
:param content: the content to be scanned for mentions
:param look_in: dictionary with name, id and class_. only element matching all of these will be scanned
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers: dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: dictionary of Mentions
"""
__doc__ = None
if test_urls:
URLValidator(message='invalid source URL')(sourceURL)
if content:
result = {'status': requests.codes.ok,
'headers': None,
}
else:
r = requests.get(sourceURL, verify=True, headers=headers, timeout=timeout)
result = {'status': r.status_code,
'headers': r.headers
}
# Check for character encodings and use 'correct' data
if 'charset' in r.headers.get('content-type', ''):
content = r.text
else:
content = r.content
result.update({'refs': set(), 'post-url': sourceURL})
if result['status'] == requests.codes.ok:
# Allow passing BS doc as content
if isinstance(content, BeautifulSoup):
__doc__ = content
# result.update({'content': unicode(__doc__)})
result.update({'content': str(__doc__)})
else:
__doc__ = BeautifulSoup(content, _html_parser)
result.update({'content': content})
# try to find first h-entry else use full document
entry = __doc__.find(class_="h-entry") or __doc__
# Allow finding particular URL
if targetURL:
# find only targetURL
all_links = entry.find_all('a', href=targetURL)
else:
# find all links with a href
all_links = entry.find_all('a', href=True)
for link in all_links:
href = link.get('href', None)
if href:
url = urlparse(href)
if url.scheme in ('http', 'https'):
if url.hostname and url.hostname not in exclude_domains:
result['refs'].add(href)
return result
|
python
|
def findMentions(sourceURL, targetURL=None, exclude_domains=[], content=None, test_urls=True, headers={}, timeout=None):
"""Find all <a /> elements in the given html for a post. Only scan html element matching all criteria in look_in.
optionally the content to be scanned can be given as an argument.
If any have an href attribute that is not from the
one of the items in exclude_domains, append it to our lists.
:param sourceURL: the URL for the post we are scanning
:param exclude_domains: a list of domains to exclude from the search
:type exclude_domains: list
:param content: the content to be scanned for mentions
:param look_in: dictionary with name, id and class_. only element matching all of these will be scanned
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers: dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: dictionary of Mentions
"""
__doc__ = None
if test_urls:
URLValidator(message='invalid source URL')(sourceURL)
if content:
result = {'status': requests.codes.ok,
'headers': None,
}
else:
r = requests.get(sourceURL, verify=True, headers=headers, timeout=timeout)
result = {'status': r.status_code,
'headers': r.headers
}
# Check for character encodings and use 'correct' data
if 'charset' in r.headers.get('content-type', ''):
content = r.text
else:
content = r.content
result.update({'refs': set(), 'post-url': sourceURL})
if result['status'] == requests.codes.ok:
# Allow passing BS doc as content
if isinstance(content, BeautifulSoup):
__doc__ = content
# result.update({'content': unicode(__doc__)})
result.update({'content': str(__doc__)})
else:
__doc__ = BeautifulSoup(content, _html_parser)
result.update({'content': content})
# try to find first h-entry else use full document
entry = __doc__.find(class_="h-entry") or __doc__
# Allow finding particular URL
if targetURL:
# find only targetURL
all_links = entry.find_all('a', href=targetURL)
else:
# find all links with a href
all_links = entry.find_all('a', href=True)
for link in all_links:
href = link.get('href', None)
if href:
url = urlparse(href)
if url.scheme in ('http', 'https'):
if url.hostname and url.hostname not in exclude_domains:
result['refs'].add(href)
return result
|
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optionally the content to be scanned can be given as an argument.
If any have an href attribute that is not from the
one of the items in exclude_domains, append it to our lists.
:param sourceURL: the URL for the post we are scanning
:param exclude_domains: a list of domains to exclude from the search
:type exclude_domains: list
:param content: the content to be scanned for mentions
:param look_in: dictionary with name, id and class_. only element matching all of these will be scanned
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers: dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: dictionary of Mentions
|
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"."
] |
train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/webmention.py#L41-L112
|
bear/ronkyuu
|
ronkyuu/webmention.py
|
findEndpoint
|
def findEndpoint(html):
"""Search the given html content for all <link /> elements
and return any discovered WebMention URL.
:param html: html content
:rtype: WebMention URL
"""
poss_rels = ['webmention', 'http://webmention.org', 'http://webmention.org/', 'https://webmention.org', 'https://webmention.org/']
# find elements with correct rels and a href value
all_links = BeautifulSoup(html, _html_parser).find_all(rel=poss_rels, href=True)
for link in all_links:
s = link.get('href', None)
if s is not None:
return s
return None
|
python
|
def findEndpoint(html):
"""Search the given html content for all <link /> elements
and return any discovered WebMention URL.
:param html: html content
:rtype: WebMention URL
"""
poss_rels = ['webmention', 'http://webmention.org', 'http://webmention.org/', 'https://webmention.org', 'https://webmention.org/']
# find elements with correct rels and a href value
all_links = BeautifulSoup(html, _html_parser).find_all(rel=poss_rels, href=True)
for link in all_links:
s = link.get('href', None)
if s is not None:
return s
return None
|
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Search the given html content for all <link /> elements
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|
[
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train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/webmention.py#L115-L131
|
bear/ronkyuu
|
ronkyuu/webmention.py
|
discoverEndpoint
|
def discoverEndpoint(url, test_urls=True, headers={}, timeout=None, request=None, debug=False):
"""Discover any WebMention endpoint for a given URL.
:param link: URL to discover WebMention endpoint
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:param request: optional Requests request object to avoid another GET
:rtype: tuple (status_code, URL, [debug])
"""
if test_urls:
URLValidator(message='invalid URL')(url)
# status, webmention
endpointURL = None
debugOutput = []
try:
if request is not None:
targetRequest = request
else:
targetRequest = requests.get(url, verify=False, headers=headers, timeout=timeout)
returnCode = targetRequest.status_code
debugOutput.append('%s %s' % (returnCode, url))
if returnCode == requests.codes.ok:
try:
linkHeader = parse_link_header(targetRequest.headers['link'])
endpointURL = linkHeader.get('webmention', '') or \
linkHeader.get('http://webmention.org', '') or \
linkHeader.get('http://webmention.org/', '') or \
linkHeader.get('https://webmention.org', '') or \
linkHeader.get('https://webmention.org/', '')
# force searching in the HTML if not found
if not endpointURL:
raise AttributeError
debugOutput.append('found in link headers')
except (KeyError, AttributeError):
endpointURL = findEndpoint(targetRequest.text)
debugOutput.append('found in body')
if endpointURL is not None:
endpointURL = urljoin(url, endpointURL)
except (requests.exceptions.RequestException, requests.exceptions.ConnectionError,
requests.exceptions.HTTPError, requests.exceptions.URLRequired,
requests.exceptions.TooManyRedirects, requests.exceptions.Timeout):
debugOutput.append('exception during GET request')
returnCode = 500
debugOutput.append('endpointURL: %s %s' % (returnCode, endpointURL))
if debug:
return (returnCode, endpointURL, debugOutput)
else:
return (returnCode, endpointURL)
|
python
|
def discoverEndpoint(url, test_urls=True, headers={}, timeout=None, request=None, debug=False):
"""Discover any WebMention endpoint for a given URL.
:param link: URL to discover WebMention endpoint
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:param request: optional Requests request object to avoid another GET
:rtype: tuple (status_code, URL, [debug])
"""
if test_urls:
URLValidator(message='invalid URL')(url)
# status, webmention
endpointURL = None
debugOutput = []
try:
if request is not None:
targetRequest = request
else:
targetRequest = requests.get(url, verify=False, headers=headers, timeout=timeout)
returnCode = targetRequest.status_code
debugOutput.append('%s %s' % (returnCode, url))
if returnCode == requests.codes.ok:
try:
linkHeader = parse_link_header(targetRequest.headers['link'])
endpointURL = linkHeader.get('webmention', '') or \
linkHeader.get('http://webmention.org', '') or \
linkHeader.get('http://webmention.org/', '') or \
linkHeader.get('https://webmention.org', '') or \
linkHeader.get('https://webmention.org/', '')
# force searching in the HTML if not found
if not endpointURL:
raise AttributeError
debugOutput.append('found in link headers')
except (KeyError, AttributeError):
endpointURL = findEndpoint(targetRequest.text)
debugOutput.append('found in body')
if endpointURL is not None:
endpointURL = urljoin(url, endpointURL)
except (requests.exceptions.RequestException, requests.exceptions.ConnectionError,
requests.exceptions.HTTPError, requests.exceptions.URLRequired,
requests.exceptions.TooManyRedirects, requests.exceptions.Timeout):
debugOutput.append('exception during GET request')
returnCode = 500
debugOutput.append('endpointURL: %s %s' % (returnCode, endpointURL))
if debug:
return (returnCode, endpointURL, debugOutput)
else:
return (returnCode, endpointURL)
|
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Discover any WebMention endpoint for a given URL.
:param link: URL to discover WebMention endpoint
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:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:param request: optional Requests request object to avoid another GET
:rtype: tuple (status_code, URL, [debug])
|
[
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"."
] |
train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/webmention.py#L134-L185
|
bear/ronkyuu
|
ronkyuu/webmention.py
|
sendWebmention
|
def sendWebmention(sourceURL, targetURL, webmention=None, test_urls=True, vouchDomain=None,
headers={}, timeout=None, debug=False):
"""Send to the :targetURL: a WebMention for the :sourceURL:
The WebMention will be discovered if not given in the :webmention:
parameter.
:param sourceURL: URL that is referencing :targetURL:
:param targetURL: URL of mentioned post
:param webmention: optional WebMention endpoint
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: HTTPrequest object if WebMention endpoint was valid
"""
if test_urls:
v = URLValidator()
v(sourceURL)
v(targetURL)
debugOutput = []
originalURL = targetURL
try:
targetRequest = requests.get(targetURL)
if targetRequest.status_code == requests.codes.ok:
if len(targetRequest.history) > 0:
redirect = targetRequest.history[-1]
if (redirect.status_code == 301 or redirect.status_code == 302) and 'Location' in redirect.headers:
targetURL = urljoin(targetURL, redirect.headers['Location'])
debugOutput.append('targetURL redirected: %s' % targetURL)
if webmention is None:
wStatus, wUrl = discoverEndpoint(targetURL, headers=headers, timeout=timeout, request=targetRequest)
else:
wStatus = 200
wUrl = webmention
debugOutput.append('endpointURL: %s %s' % (wStatus, wUrl))
if wStatus == requests.codes.ok and wUrl is not None:
if test_urls:
v(wUrl)
payload = {'source': sourceURL,
'target': originalURL}
if vouchDomain is not None:
payload['vouch'] = vouchDomain
try:
result = requests.post(wUrl, data=payload, headers=headers, timeout=timeout)
debugOutput.append('POST %s -- %s' % (wUrl, result.status_code))
if result.status_code == 405 and len(result.history) > 0:
redirect = result.history[-1]
if redirect.status_code == 301 and 'Location' in redirect.headers:
result = requests.post(redirect.headers['Location'], data=payload, headers=headers, timeout=timeout)
debugOutput.append('redirected POST %s -- %s' % (redirect.headers['Location'], result.status_code))
except Exception as e:
result = None
except (requests.exceptions.RequestException, requests.exceptions.ConnectionError,
requests.exceptions.HTTPError, requests.exceptions.URLRequired,
requests.exceptions.TooManyRedirects, requests.exceptions.Timeout):
debugOutput.append('exception during GET request')
result = None
return result
|
python
|
def sendWebmention(sourceURL, targetURL, webmention=None, test_urls=True, vouchDomain=None,
headers={}, timeout=None, debug=False):
"""Send to the :targetURL: a WebMention for the :sourceURL:
The WebMention will be discovered if not given in the :webmention:
parameter.
:param sourceURL: URL that is referencing :targetURL:
:param targetURL: URL of mentioned post
:param webmention: optional WebMention endpoint
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: HTTPrequest object if WebMention endpoint was valid
"""
if test_urls:
v = URLValidator()
v(sourceURL)
v(targetURL)
debugOutput = []
originalURL = targetURL
try:
targetRequest = requests.get(targetURL)
if targetRequest.status_code == requests.codes.ok:
if len(targetRequest.history) > 0:
redirect = targetRequest.history[-1]
if (redirect.status_code == 301 or redirect.status_code == 302) and 'Location' in redirect.headers:
targetURL = urljoin(targetURL, redirect.headers['Location'])
debugOutput.append('targetURL redirected: %s' % targetURL)
if webmention is None:
wStatus, wUrl = discoverEndpoint(targetURL, headers=headers, timeout=timeout, request=targetRequest)
else:
wStatus = 200
wUrl = webmention
debugOutput.append('endpointURL: %s %s' % (wStatus, wUrl))
if wStatus == requests.codes.ok and wUrl is not None:
if test_urls:
v(wUrl)
payload = {'source': sourceURL,
'target': originalURL}
if vouchDomain is not None:
payload['vouch'] = vouchDomain
try:
result = requests.post(wUrl, data=payload, headers=headers, timeout=timeout)
debugOutput.append('POST %s -- %s' % (wUrl, result.status_code))
if result.status_code == 405 and len(result.history) > 0:
redirect = result.history[-1]
if redirect.status_code == 301 and 'Location' in redirect.headers:
result = requests.post(redirect.headers['Location'], data=payload, headers=headers, timeout=timeout)
debugOutput.append('redirected POST %s -- %s' % (redirect.headers['Location'], result.status_code))
except Exception as e:
result = None
except (requests.exceptions.RequestException, requests.exceptions.ConnectionError,
requests.exceptions.HTTPError, requests.exceptions.URLRequired,
requests.exceptions.TooManyRedirects, requests.exceptions.Timeout):
debugOutput.append('exception during GET request')
result = None
return result
|
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parameter.
:param sourceURL: URL that is referencing :targetURL:
:param targetURL: URL of mentioned post
:param webmention: optional WebMention endpoint
:param test_urls: optional flag to test URLs for validation
:param headers: optional headers to send with any web requests
:type headers dict
:param timeout: optional timeout for web requests
:type timeout float
:rtype: HTTPrequest object if WebMention endpoint was valid
|
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] |
train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/webmention.py#L187-L249
|
bear/ronkyuu
|
ronkyuu/tools.py
|
parse_link_header
|
def parse_link_header(link):
"""takes the link header as a string and returns a dictionary with rel values as keys and urls as values
:param link: link header as a string
:rtype: dictionary {rel_name: rel_value}
"""
rel_dict = {}
for rels in link.split(','):
rel_break = quoted_split(rels, ';')
try:
rel_url = re.search('<(.+?)>', rel_break[0]).group(1)
rel_names = quoted_split(rel_break[1], '=')[-1]
if rel_names.startswith('"') and rel_names.endswith('"'):
rel_names = rel_names[1:-1]
for name in rel_names.split():
rel_dict[name] = rel_url
except (AttributeError, IndexError):
pass
return rel_dict
|
python
|
def parse_link_header(link):
"""takes the link header as a string and returns a dictionary with rel values as keys and urls as values
:param link: link header as a string
:rtype: dictionary {rel_name: rel_value}
"""
rel_dict = {}
for rels in link.split(','):
rel_break = quoted_split(rels, ';')
try:
rel_url = re.search('<(.+?)>', rel_break[0]).group(1)
rel_names = quoted_split(rel_break[1], '=')[-1]
if rel_names.startswith('"') and rel_names.endswith('"'):
rel_names = rel_names[1:-1]
for name in rel_names.split():
rel_dict[name] = rel_url
except (AttributeError, IndexError):
pass
return rel_dict
|
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|
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train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/tools.py#L86-L104
|
bear/ronkyuu
|
ronkyuu/relme.py
|
findRelMe
|
def findRelMe(sourceURL):
"""Find all <a /> elements in the given html for a post.
If any have an href attribute that is rel="me" then include
it in the result.
:param sourceURL: the URL for the post we are scanning
:rtype: dictionary of RelMe references
"""
r = requests.get(sourceURL)
result = {'status': r.status_code,
'headers': r.headers,
'history': r.history,
'content': r.text,
'relme': [],
'url': sourceURL
}
if r.status_code == requests.codes.ok:
dom = BeautifulSoup(r.text, _html_parser)
for link in dom.find_all('a', rel='me'):
rel = link.get('rel')
href = link.get('href')
if rel is not None and href is not None:
url = urlparse(href)
if url is not None and url.scheme in ('http', 'https'):
result['relme'].append(cleanURL(href))
return result
|
python
|
def findRelMe(sourceURL):
"""Find all <a /> elements in the given html for a post.
If any have an href attribute that is rel="me" then include
it in the result.
:param sourceURL: the URL for the post we are scanning
:rtype: dictionary of RelMe references
"""
r = requests.get(sourceURL)
result = {'status': r.status_code,
'headers': r.headers,
'history': r.history,
'content': r.text,
'relme': [],
'url': sourceURL
}
if r.status_code == requests.codes.ok:
dom = BeautifulSoup(r.text, _html_parser)
for link in dom.find_all('a', rel='me'):
rel = link.get('rel')
href = link.get('href')
if rel is not None and href is not None:
url = urlparse(href)
if url is not None and url.scheme in ('http', 'https'):
result['relme'].append(cleanURL(href))
return result
|
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:param sourceURL: the URL for the post we are scanning
:rtype: dictionary of RelMe references
|
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] |
train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/relme.py#L63-L89
|
bear/ronkyuu
|
ronkyuu/relme.py
|
confirmRelMe
|
def confirmRelMe(profileURL, resourceURL, profileRelMes=None, resourceRelMes=None):
"""Determine if a given :resourceURL: is authoritative for the :profileURL:
TODO add https/http filtering for those who wish to limit/restrict urls to match fully
TODO add code to ensure that each item in the redirect chain is authoritative
:param profileURL: URL of the user
:param resourceURL: URL of the resource to validate
:param profileRelMes: optional list of rel="me" links within the profile URL
:param resourceRelMes: optional list of rel="me" links found within resource URL
:rtype: True if confirmed
"""
result = False
profile = normalizeURL(profileURL)
if profileRelMes is None:
profileRelMe = findRelMe(profileURL)
profileRelMes = profileRelMe['relme']
if resourceRelMes is None:
resourceRelMe = findRelMe(resourceURL)
resourceRelMes = resourceRelMe['relme']
for url in resourceRelMes:
if profile in (url, normalizeURL(url)):
result = True
break
return result
|
python
|
def confirmRelMe(profileURL, resourceURL, profileRelMes=None, resourceRelMes=None):
"""Determine if a given :resourceURL: is authoritative for the :profileURL:
TODO add https/http filtering for those who wish to limit/restrict urls to match fully
TODO add code to ensure that each item in the redirect chain is authoritative
:param profileURL: URL of the user
:param resourceURL: URL of the resource to validate
:param profileRelMes: optional list of rel="me" links within the profile URL
:param resourceRelMes: optional list of rel="me" links found within resource URL
:rtype: True if confirmed
"""
result = False
profile = normalizeURL(profileURL)
if profileRelMes is None:
profileRelMe = findRelMe(profileURL)
profileRelMes = profileRelMe['relme']
if resourceRelMes is None:
resourceRelMe = findRelMe(resourceURL)
resourceRelMes = resourceRelMe['relme']
for url in resourceRelMes:
if profile in (url, normalizeURL(url)):
result = True
break
return result
|
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Determine if a given :resourceURL: is authoritative for the :profileURL:
TODO add https/http filtering for those who wish to limit/restrict urls to match fully
TODO add code to ensure that each item in the redirect chain is authoritative
:param profileURL: URL of the user
:param resourceURL: URL of the resource to validate
:param profileRelMes: optional list of rel="me" links within the profile URL
:param resourceRelMes: optional list of rel="me" links found within resource URL
:rtype: True if confirmed
|
[
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":",
"resourceURL",
":",
"is",
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"for",
"the",
":",
"profileURL",
":"
] |
train
|
https://github.com/bear/ronkyuu/blob/91a05fbe220b661760467b7b3d3d780a9ba28afa/ronkyuu/relme.py#L92-L119
|
alexras/bread
|
bread/utils.py
|
indent_text
|
def indent_text(string, indent_level=2):
"""Indent every line of text in a newline-delimited string"""
indented_lines = []
indent_spaces = ' ' * indent_level
for line in string.split('\n'):
indented_lines.append(indent_spaces + line)
return '\n'.join(indented_lines)
|
python
|
def indent_text(string, indent_level=2):
"""Indent every line of text in a newline-delimited string"""
indented_lines = []
indent_spaces = ' ' * indent_level
for line in string.split('\n'):
indented_lines.append(indent_spaces + line)
return '\n'.join(indented_lines)
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train
|
https://github.com/alexras/bread/blob/2e131380878c07500167fc12685e7bff1df258a4/bread/utils.py#L1-L10
|
takluyver/requests_download
|
requests_download.py
|
download
|
def download(url, target, headers=None, trackers=()):
"""Download a file using requests.
This is like urllib.request.urlretrieve, but:
- requests validates SSL certificates by default
- you can pass tracker objects to e.g. display a progress bar or calculate
a file hash.
"""
if headers is None:
headers = {}
headers.setdefault('user-agent', 'requests_download/'+__version__)
r = requests.get(url, headers=headers, stream=True)
r.raise_for_status()
for t in trackers:
t.on_start(r)
with open(target, 'wb') as f:
for chunk in r.iter_content(chunk_size=8192):
if chunk:
f.write(chunk)
for t in trackers:
t.on_chunk(chunk)
for t in trackers:
t.on_finish()
|
python
|
def download(url, target, headers=None, trackers=()):
"""Download a file using requests.
This is like urllib.request.urlretrieve, but:
- requests validates SSL certificates by default
- you can pass tracker objects to e.g. display a progress bar or calculate
a file hash.
"""
if headers is None:
headers = {}
headers.setdefault('user-agent', 'requests_download/'+__version__)
r = requests.get(url, headers=headers, stream=True)
r.raise_for_status()
for t in trackers:
t.on_start(r)
with open(target, 'wb') as f:
for chunk in r.iter_content(chunk_size=8192):
if chunk:
f.write(chunk)
for t in trackers:
t.on_chunk(chunk)
for t in trackers:
t.on_finish()
|
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|
[
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"."
] |
train
|
https://github.com/takluyver/requests_download/blob/bc0412bb930051af21ab1959402abab883c78e76/requests_download.py#L65-L91
|
alexras/bread
|
bread/lifecycle.py
|
write
|
def write(parsed_obj, spec=None, filename=None):
"""Writes an object created by `parse` to either a file or a bytearray.
If the object doesn't end on a byte boundary, zeroes are appended to it
until it does.
"""
if not isinstance(parsed_obj, BreadStruct):
raise ValueError(
'Object to write must be a structure created '
'by bread.parse')
if filename is not None:
with open(filename, 'wb') as fp:
parsed_obj._data_bits[:parsed_obj._length].tofile(fp)
else:
return bytearray(parsed_obj._data_bits[:parsed_obj._length].tobytes())
|
python
|
def write(parsed_obj, spec=None, filename=None):
"""Writes an object created by `parse` to either a file or a bytearray.
If the object doesn't end on a byte boundary, zeroes are appended to it
until it does.
"""
if not isinstance(parsed_obj, BreadStruct):
raise ValueError(
'Object to write must be a structure created '
'by bread.parse')
if filename is not None:
with open(filename, 'wb') as fp:
parsed_obj._data_bits[:parsed_obj._length].tofile(fp)
else:
return bytearray(parsed_obj._data_bits[:parsed_obj._length].tobytes())
|
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Writes an object created by `parse` to either a file or a bytearray.
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train
|
https://github.com/alexras/bread/blob/2e131380878c07500167fc12685e7bff1df258a4/bread/lifecycle.py#L41-L56
|
audreyr/alotofeffort
|
alotofeffort/send.py
|
deploy_file
|
def deploy_file(file_path, bucket):
""" Uploads a file to an S3 bucket, as a public file. """
# Paths look like:
# index.html
# css/bootstrap.min.css
logger.info("Deploying {0}".format(file_path))
# Upload the actual file to file_path
k = Key(bucket)
k.key = file_path
try:
k.set_contents_from_filename(file_path)
k.set_acl('public-read')
except socket.error:
logger.warning("Caught socket.error while trying to upload {0}".format(
file_path))
msg = "Please file an issue with alotofeffort if you see this,"
logger.warning(msg)
logger.warning("providing as much info as you can.")
|
python
|
def deploy_file(file_path, bucket):
""" Uploads a file to an S3 bucket, as a public file. """
# Paths look like:
# index.html
# css/bootstrap.min.css
logger.info("Deploying {0}".format(file_path))
# Upload the actual file to file_path
k = Key(bucket)
k.key = file_path
try:
k.set_contents_from_filename(file_path)
k.set_acl('public-read')
except socket.error:
logger.warning("Caught socket.error while trying to upload {0}".format(
file_path))
msg = "Please file an issue with alotofeffort if you see this,"
logger.warning(msg)
logger.warning("providing as much info as you can.")
|
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train
|
https://github.com/audreyr/alotofeffort/blob/06deca82a70fa9896496fd44c8c6f24707396c50/alotofeffort/send.py#L15-L35
|
audreyr/alotofeffort
|
alotofeffort/send.py
|
deploy
|
def deploy(www_dir, bucket_name):
""" Deploy to the configured S3 bucket. """
# Set up the connection to an S3 bucket.
conn = boto.connect_s3()
bucket = conn.get_bucket(bucket_name)
# Deploy each changed file in www_dir
os.chdir(www_dir)
for root, dirs, files in os.walk('.'):
for f in files:
# Use full relative path. Normalize to remove dot.
file_path = os.path.normpath(os.path.join(root, f))
if has_changed_since_last_deploy(file_path, bucket):
deploy_file(file_path, bucket)
else:
logger.info("Skipping {0}".format(file_path))
# Make the whole bucket public
bucket.set_acl('public-read')
# Configure it to be a website
bucket.configure_website('index.html', 'error.html')
# Print the endpoint, so you know the URL
msg = "Your website is now live at {0}".format(
bucket.get_website_endpoint())
logger.info(msg)
logger.info("If you haven't done so yet, point your domain name there!")
|
python
|
def deploy(www_dir, bucket_name):
""" Deploy to the configured S3 bucket. """
# Set up the connection to an S3 bucket.
conn = boto.connect_s3()
bucket = conn.get_bucket(bucket_name)
# Deploy each changed file in www_dir
os.chdir(www_dir)
for root, dirs, files in os.walk('.'):
for f in files:
# Use full relative path. Normalize to remove dot.
file_path = os.path.normpath(os.path.join(root, f))
if has_changed_since_last_deploy(file_path, bucket):
deploy_file(file_path, bucket)
else:
logger.info("Skipping {0}".format(file_path))
# Make the whole bucket public
bucket.set_acl('public-read')
# Configure it to be a website
bucket.configure_website('index.html', 'error.html')
# Print the endpoint, so you know the URL
msg = "Your website is now live at {0}".format(
bucket.get_website_endpoint())
logger.info(msg)
logger.info("If you haven't done so yet, point your domain name there!")
|
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[
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train
|
https://github.com/audreyr/alotofeffort/blob/06deca82a70fa9896496fd44c8c6f24707396c50/alotofeffort/send.py#L38-L67
|
audreyr/alotofeffort
|
alotofeffort/send.py
|
has_changed_since_last_deploy
|
def has_changed_since_last_deploy(file_path, bucket):
"""
Checks if a file has changed since the last time it was deployed.
:param file_path: Path to file which should be checked. Should be relative
from root of bucket.
:param bucket_name: Name of S3 bucket to check against.
:returns: True if the file has changed, else False.
"""
msg = "Checking if {0} has changed since last deploy.".format(file_path)
logger.debug(msg)
with open(file_path) as f:
data = f.read()
file_md5 = hashlib.md5(data.encode('utf-8')).hexdigest()
logger.debug("file_md5 is {0}".format(file_md5))
key = bucket.get_key(file_path)
# HACK: Boto's md5 property does not work when the file hasn't been
# downloaded. The etag works but will break for multi-part uploaded files.
# http://stackoverflow.com/questions/16872679/how-to-programmatically-
# get-the-md5-checksum-of-amazon-s3-file-using-boto/17607096#17607096
# Also the double quotes around it must be stripped. Sketchy...boto's fault
if key:
key_md5 = key.etag.replace('"', '').strip()
logger.debug("key_md5 is {0}".format(key_md5))
else:
logger.debug("File does not exist in bucket")
return True
if file_md5 == key_md5:
logger.debug("File has not changed.")
return False
logger.debug("File has changed.")
return True
|
python
|
def has_changed_since_last_deploy(file_path, bucket):
"""
Checks if a file has changed since the last time it was deployed.
:param file_path: Path to file which should be checked. Should be relative
from root of bucket.
:param bucket_name: Name of S3 bucket to check against.
:returns: True if the file has changed, else False.
"""
msg = "Checking if {0} has changed since last deploy.".format(file_path)
logger.debug(msg)
with open(file_path) as f:
data = f.read()
file_md5 = hashlib.md5(data.encode('utf-8')).hexdigest()
logger.debug("file_md5 is {0}".format(file_md5))
key = bucket.get_key(file_path)
# HACK: Boto's md5 property does not work when the file hasn't been
# downloaded. The etag works but will break for multi-part uploaded files.
# http://stackoverflow.com/questions/16872679/how-to-programmatically-
# get-the-md5-checksum-of-amazon-s3-file-using-boto/17607096#17607096
# Also the double quotes around it must be stripped. Sketchy...boto's fault
if key:
key_md5 = key.etag.replace('"', '').strip()
logger.debug("key_md5 is {0}".format(key_md5))
else:
logger.debug("File does not exist in bucket")
return True
if file_md5 == key_md5:
logger.debug("File has not changed.")
return False
logger.debug("File has changed.")
return True
|
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|
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train
|
https://github.com/audreyr/alotofeffort/blob/06deca82a70fa9896496fd44c8c6f24707396c50/alotofeffort/send.py#L70-L105
|
audreyr/alotofeffort
|
alotofeffort/main.py
|
main
|
def main():
""" Entry point for the package, as defined in setup.py. """
# Log info and above to console
logging.basicConfig(
format='%(levelname)s: %(message)s', level=logging.INFO)
# Get command line input/output arguments
msg = 'Instantly deploy static HTML sites to S3 at the command line.'
parser = argparse.ArgumentParser(description=msg)
parser.add_argument(
'www_dir',
help='Directory containing the HTML files for your website.'
)
parser.add_argument(
'bucket_name',
help='Name of S3 bucket to deploy to, e.g. mybucket.'
)
args = parser.parse_args()
# Deploy the site to S3!
deploy(args.www_dir, args.bucket_name)
|
python
|
def main():
""" Entry point for the package, as defined in setup.py. """
# Log info and above to console
logging.basicConfig(
format='%(levelname)s: %(message)s', level=logging.INFO)
# Get command line input/output arguments
msg = 'Instantly deploy static HTML sites to S3 at the command line.'
parser = argparse.ArgumentParser(description=msg)
parser.add_argument(
'www_dir',
help='Directory containing the HTML files for your website.'
)
parser.add_argument(
'bucket_name',
help='Name of S3 bucket to deploy to, e.g. mybucket.'
)
args = parser.parse_args()
# Deploy the site to S3!
deploy(args.www_dir, args.bucket_name)
|
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"'www_dir'",
",",
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"=",
"'Directory containing the HTML files for your website.'",
")",
"parser",
".",
"add_argument",
"(",
"'bucket_name'",
",",
"help",
"=",
"'Name of S3 bucket to deploy to, e.g. mybucket.'",
")",
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"parse_args",
"(",
")",
"# Deploy the site to S3!",
"deploy",
"(",
"args",
".",
"www_dir",
",",
"args",
".",
"bucket_name",
")"
] |
Entry point for the package, as defined in setup.py.
|
[
"Entry",
"point",
"for",
"the",
"package",
"as",
"defined",
"in",
"setup",
".",
"py",
"."
] |
train
|
https://github.com/audreyr/alotofeffort/blob/06deca82a70fa9896496fd44c8c6f24707396c50/alotofeffort/main.py#L9-L30
|
rainmanwy/robotframework-SikuliLibrary
|
src/python/sikuli.py
|
SikuliLibrary.start_sikuli_process
|
def start_sikuli_process(self, port=None):
"""
This keyword is used to start sikuli java process.
If library is inited with mode "OLD", sikuli java process is started automatically.
If library is inited with mode "NEW", this keyword should be used.
:param port: port of sikuli java process, if value is None or 0, a random free port will be used
:return: None
"""
if port is None or int(port) == 0:
port = self._get_free_tcp_port()
self.port = port
start_retries = 0
started = False
while start_retries < 5:
try:
self._start_sikuli_java_process()
except RuntimeError as err:
print('error........%s' % err)
if self.process:
self.process.terminate_process()
self.port = self._get_free_tcp_port()
start_retries += 1
continue
started = True
break
if not started:
raise RuntimeError('Start sikuli java process failed!')
self.remote = self._connect_remote_library()
|
python
|
def start_sikuli_process(self, port=None):
"""
This keyword is used to start sikuli java process.
If library is inited with mode "OLD", sikuli java process is started automatically.
If library is inited with mode "NEW", this keyword should be used.
:param port: port of sikuli java process, if value is None or 0, a random free port will be used
:return: None
"""
if port is None or int(port) == 0:
port = self._get_free_tcp_port()
self.port = port
start_retries = 0
started = False
while start_retries < 5:
try:
self._start_sikuli_java_process()
except RuntimeError as err:
print('error........%s' % err)
if self.process:
self.process.terminate_process()
self.port = self._get_free_tcp_port()
start_retries += 1
continue
started = True
break
if not started:
raise RuntimeError('Start sikuli java process failed!')
self.remote = self._connect_remote_library()
|
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"(",
")"
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This keyword is used to start sikuli java process.
If library is inited with mode "OLD", sikuli java process is started automatically.
If library is inited with mode "NEW", this keyword should be used.
:param port: port of sikuli java process, if value is None or 0, a random free port will be used
:return: None
|
[
"This",
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"java",
"process",
".",
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"process",
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"is",
"inited",
"with",
"mode",
"NEW",
"this",
"keyword",
"should",
"be",
"used",
"."
] |
train
|
https://github.com/rainmanwy/robotframework-SikuliLibrary/blob/992874dd96b139246a62fb07ec763e0a4caffad8/src/python/sikuli.py#L65-L93
|
JamesRitchie/django-rest-framework-expiring-tokens
|
rest_framework_expiring_authtoken/views.py
|
ObtainExpiringAuthToken.post
|
def post(self, request):
"""Respond to POSTed username/password with token."""
serializer = AuthTokenSerializer(data=request.data)
if serializer.is_valid():
token, _ = ExpiringToken.objects.get_or_create(
user=serializer.validated_data['user']
)
if token.expired():
# If the token is expired, generate a new one.
token.delete()
token = ExpiringToken.objects.create(
user=serializer.validated_data['user']
)
data = {'token': token.key}
return Response(data)
return Response(serializer.errors, status=HTTP_400_BAD_REQUEST)
|
python
|
def post(self, request):
"""Respond to POSTed username/password with token."""
serializer = AuthTokenSerializer(data=request.data)
if serializer.is_valid():
token, _ = ExpiringToken.objects.get_or_create(
user=serializer.validated_data['user']
)
if token.expired():
# If the token is expired, generate a new one.
token.delete()
token = ExpiringToken.objects.create(
user=serializer.validated_data['user']
)
data = {'token': token.key}
return Response(data)
return Response(serializer.errors, status=HTTP_400_BAD_REQUEST)
|
[
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",",
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")",
":",
"serializer",
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"AuthTokenSerializer",
"(",
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".",
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")",
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"(",
")",
":",
"token",
",",
"_",
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"[",
"'user'",
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")",
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".",
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"return",
"Response",
"(",
"serializer",
".",
"errors",
",",
"status",
"=",
"HTTP_400_BAD_REQUEST",
")"
] |
Respond to POSTed username/password with token.
|
[
"Respond",
"to",
"POSTed",
"username",
"/",
"password",
"with",
"token",
"."
] |
train
|
https://github.com/JamesRitchie/django-rest-framework-expiring-tokens/blob/e62f1f92a621575174172e970da624d367ac0cf6/rest_framework_expiring_authtoken/views.py#L20-L39
|
JamesRitchie/django-rest-framework-expiring-tokens
|
rest_framework_expiring_authtoken/settings.py
|
TokenSettings.EXPIRING_TOKEN_LIFESPAN
|
def EXPIRING_TOKEN_LIFESPAN(self):
"""
Return the allowed lifespan of a token as a TimeDelta object.
Defaults to 30 days.
"""
try:
val = settings.EXPIRING_TOKEN_LIFESPAN
except AttributeError:
val = timedelta(days=30)
return val
|
python
|
def EXPIRING_TOKEN_LIFESPAN(self):
"""
Return the allowed lifespan of a token as a TimeDelta object.
Defaults to 30 days.
"""
try:
val = settings.EXPIRING_TOKEN_LIFESPAN
except AttributeError:
val = timedelta(days=30)
return val
|
[
"def",
"EXPIRING_TOKEN_LIFESPAN",
"(",
"self",
")",
":",
"try",
":",
"val",
"=",
"settings",
".",
"EXPIRING_TOKEN_LIFESPAN",
"except",
"AttributeError",
":",
"val",
"=",
"timedelta",
"(",
"days",
"=",
"30",
")",
"return",
"val"
] |
Return the allowed lifespan of a token as a TimeDelta object.
Defaults to 30 days.
|
[
"Return",
"the",
"allowed",
"lifespan",
"of",
"a",
"token",
"as",
"a",
"TimeDelta",
"object",
"."
] |
train
|
https://github.com/JamesRitchie/django-rest-framework-expiring-tokens/blob/e62f1f92a621575174172e970da624d367ac0cf6/rest_framework_expiring_authtoken/settings.py#L16-L27
|
JamesRitchie/django-rest-framework-expiring-tokens
|
rest_framework_expiring_authtoken/models.py
|
ExpiringToken.expired
|
def expired(self):
"""Return boolean indicating token expiration."""
now = timezone.now()
if self.created < now - token_settings.EXPIRING_TOKEN_LIFESPAN:
return True
return False
|
python
|
def expired(self):
"""Return boolean indicating token expiration."""
now = timezone.now()
if self.created < now - token_settings.EXPIRING_TOKEN_LIFESPAN:
return True
return False
|
[
"def",
"expired",
"(",
"self",
")",
":",
"now",
"=",
"timezone",
".",
"now",
"(",
")",
"if",
"self",
".",
"created",
"<",
"now",
"-",
"token_settings",
".",
"EXPIRING_TOKEN_LIFESPAN",
":",
"return",
"True",
"return",
"False"
] |
Return boolean indicating token expiration.
|
[
"Return",
"boolean",
"indicating",
"token",
"expiration",
"."
] |
train
|
https://github.com/JamesRitchie/django-rest-framework-expiring-tokens/blob/e62f1f92a621575174172e970da624d367ac0cf6/rest_framework_expiring_authtoken/models.py#L21-L26
|
commonsense/metanl
|
metanl/extprocess.py
|
unicode_is_punctuation
|
def unicode_is_punctuation(text):
"""
Test if a token is made entirely of Unicode characters of the following
classes:
- P: punctuation
- S: symbols
- Z: separators
- M: combining marks
- C: control characters
>>> unicode_is_punctuation('word')
False
>>> unicode_is_punctuation('。')
True
>>> unicode_is_punctuation('-')
True
>>> unicode_is_punctuation('-3')
False
>>> unicode_is_punctuation('あ')
False
"""
for char in str_func(text):
category = unicodedata.category(char)[0]
if category not in 'PSZMC':
return False
return True
|
python
|
def unicode_is_punctuation(text):
"""
Test if a token is made entirely of Unicode characters of the following
classes:
- P: punctuation
- S: symbols
- Z: separators
- M: combining marks
- C: control characters
>>> unicode_is_punctuation('word')
False
>>> unicode_is_punctuation('。')
True
>>> unicode_is_punctuation('-')
True
>>> unicode_is_punctuation('-3')
False
>>> unicode_is_punctuation('あ')
False
"""
for char in str_func(text):
category = unicodedata.category(char)[0]
if category not in 'PSZMC':
return False
return True
|
[
"def",
"unicode_is_punctuation",
"(",
"text",
")",
":",
"for",
"char",
"in",
"str_func",
"(",
"text",
")",
":",
"category",
"=",
"unicodedata",
".",
"category",
"(",
"char",
")",
"[",
"0",
"]",
"if",
"category",
"not",
"in",
"'PSZMC'",
":",
"return",
"False",
"return",
"True"
] |
Test if a token is made entirely of Unicode characters of the following
classes:
- P: punctuation
- S: symbols
- Z: separators
- M: combining marks
- C: control characters
>>> unicode_is_punctuation('word')
False
>>> unicode_is_punctuation('。')
True
>>> unicode_is_punctuation('-')
True
>>> unicode_is_punctuation('-3')
False
>>> unicode_is_punctuation('あ')
False
|
[
"Test",
"if",
"a",
"token",
"is",
"made",
"entirely",
"of",
"Unicode",
"characters",
"of",
"the",
"following",
"classes",
":"
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L246-L272
|
commonsense/metanl
|
metanl/extprocess.py
|
ProcessWrapper.process
|
def process(self):
"""
Store the actual process in _process. If it doesn't exist yet, create
it.
"""
if hasattr(self, '_process'):
return self._process
else:
self._process = self._get_process()
return self._process
|
python
|
def process(self):
"""
Store the actual process in _process. If it doesn't exist yet, create
it.
"""
if hasattr(self, '_process'):
return self._process
else:
self._process = self._get_process()
return self._process
|
[
"def",
"process",
"(",
"self",
")",
":",
"if",
"hasattr",
"(",
"self",
",",
"'_process'",
")",
":",
"return",
"self",
".",
"_process",
"else",
":",
"self",
".",
"_process",
"=",
"self",
".",
"_get_process",
"(",
")",
"return",
"self",
".",
"_process"
] |
Store the actual process in _process. If it doesn't exist yet, create
it.
|
[
"Store",
"the",
"actual",
"process",
"in",
"_process",
".",
"If",
"it",
"doesn",
"t",
"exist",
"yet",
"create",
"it",
"."
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L52-L61
|
commonsense/metanl
|
metanl/extprocess.py
|
ProcessWrapper._get_process
|
def _get_process(self):
"""
Create the process by running the specified command.
"""
command = self._get_command()
return subprocess.Popen(command, bufsize=-1, close_fds=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
|
python
|
def _get_process(self):
"""
Create the process by running the specified command.
"""
command = self._get_command()
return subprocess.Popen(command, bufsize=-1, close_fds=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
|
[
"def",
"_get_process",
"(",
"self",
")",
":",
"command",
"=",
"self",
".",
"_get_command",
"(",
")",
"return",
"subprocess",
".",
"Popen",
"(",
"command",
",",
"bufsize",
"=",
"-",
"1",
",",
"close_fds",
"=",
"True",
",",
"stdout",
"=",
"subprocess",
".",
"PIPE",
",",
"stdin",
"=",
"subprocess",
".",
"PIPE",
")"
] |
Create the process by running the specified command.
|
[
"Create",
"the",
"process",
"by",
"running",
"the",
"specified",
"command",
"."
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L70-L77
|
commonsense/metanl
|
metanl/extprocess.py
|
ProcessWrapper.tokenize_list
|
def tokenize_list(self, text):
"""
Split a text into separate words.
"""
return [self.get_record_token(record) for record in self.analyze(text)]
|
python
|
def tokenize_list(self, text):
"""
Split a text into separate words.
"""
return [self.get_record_token(record) for record in self.analyze(text)]
|
[
"def",
"tokenize_list",
"(",
"self",
",",
"text",
")",
":",
"return",
"[",
"self",
".",
"get_record_token",
"(",
"record",
")",
"for",
"record",
"in",
"self",
".",
"analyze",
"(",
"text",
")",
"]"
] |
Split a text into separate words.
|
[
"Split",
"a",
"text",
"into",
"separate",
"words",
"."
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L117-L121
|
commonsense/metanl
|
metanl/extprocess.py
|
ProcessWrapper.is_stopword
|
def is_stopword(self, text):
"""
Determine whether a single word is a stopword, or whether a short
phrase is made entirely of stopwords, disregarding context.
Use of this function should be avoided; it's better to give the text
in context and let the process determine which words are the stopwords.
"""
found_content_word = False
for record in self.analyze(text):
if not self.is_stopword_record(record):
found_content_word = True
break
return not found_content_word
|
python
|
def is_stopword(self, text):
"""
Determine whether a single word is a stopword, or whether a short
phrase is made entirely of stopwords, disregarding context.
Use of this function should be avoided; it's better to give the text
in context and let the process determine which words are the stopwords.
"""
found_content_word = False
for record in self.analyze(text):
if not self.is_stopword_record(record):
found_content_word = True
break
return not found_content_word
|
[
"def",
"is_stopword",
"(",
"self",
",",
"text",
")",
":",
"found_content_word",
"=",
"False",
"for",
"record",
"in",
"self",
".",
"analyze",
"(",
"text",
")",
":",
"if",
"not",
"self",
".",
"is_stopword_record",
"(",
"record",
")",
":",
"found_content_word",
"=",
"True",
"break",
"return",
"not",
"found_content_word"
] |
Determine whether a single word is a stopword, or whether a short
phrase is made entirely of stopwords, disregarding context.
Use of this function should be avoided; it's better to give the text
in context and let the process determine which words are the stopwords.
|
[
"Determine",
"whether",
"a",
"single",
"word",
"is",
"a",
"stopword",
"or",
"whether",
"a",
"short",
"phrase",
"is",
"made",
"entirely",
"of",
"stopwords",
"disregarding",
"context",
"."
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L144-L157
|
commonsense/metanl
|
metanl/extprocess.py
|
ProcessWrapper.normalize_list
|
def normalize_list(self, text, cache=None):
"""
Get a canonical list representation of text, with words
separated and reduced to their base forms.
TODO: use the cache.
"""
words = []
analysis = self.analyze(text)
for record in analysis:
if not self.is_stopword_record(record):
words.append(self.get_record_root(record))
if not words:
# Don't discard stopwords if that's all you've got
words = [self.get_record_token(record) for record in analysis]
return words
|
python
|
def normalize_list(self, text, cache=None):
"""
Get a canonical list representation of text, with words
separated and reduced to their base forms.
TODO: use the cache.
"""
words = []
analysis = self.analyze(text)
for record in analysis:
if not self.is_stopword_record(record):
words.append(self.get_record_root(record))
if not words:
# Don't discard stopwords if that's all you've got
words = [self.get_record_token(record) for record in analysis]
return words
|
[
"def",
"normalize_list",
"(",
"self",
",",
"text",
",",
"cache",
"=",
"None",
")",
":",
"words",
"=",
"[",
"]",
"analysis",
"=",
"self",
".",
"analyze",
"(",
"text",
")",
"for",
"record",
"in",
"analysis",
":",
"if",
"not",
"self",
".",
"is_stopword_record",
"(",
"record",
")",
":",
"words",
".",
"append",
"(",
"self",
".",
"get_record_root",
"(",
"record",
")",
")",
"if",
"not",
"words",
":",
"# Don't discard stopwords if that's all you've got",
"words",
"=",
"[",
"self",
".",
"get_record_token",
"(",
"record",
")",
"for",
"record",
"in",
"analysis",
"]",
"return",
"words"
] |
Get a canonical list representation of text, with words
separated and reduced to their base forms.
TODO: use the cache.
|
[
"Get",
"a",
"canonical",
"list",
"representation",
"of",
"text",
"with",
"words",
"separated",
"and",
"reduced",
"to",
"their",
"base",
"forms",
"."
] |
train
|
https://github.com/commonsense/metanl/blob/4b9ae8353489cc409bebd7e1fe10ab5b527b078e/metanl/extprocess.py#L171-L186
|
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