partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
valid | Updates.reorder | Edit the order at which statuses for the specified social media profile will
be sent out of the buffer. | buffpy/managers/updates.py | def reorder(self, updates_ids, offset=None, utc=None):
'''
Edit the order at which statuses for the specified social media profile will
be sent out of the buffer.
'''
url = PATHS['REORDER'] % self.profile_id
order_format = "order[]=%s&"
post_data = ''
if offset:
post_data +=... | def reorder(self, updates_ids, offset=None, utc=None):
'''
Edit the order at which statuses for the specified social media profile will
be sent out of the buffer.
'''
url = PATHS['REORDER'] % self.profile_id
order_format = "order[]=%s&"
post_data = ''
if offset:
post_data +=... | [
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] | vtemian/buffpy | python | https://github.com/vtemian/buffpy/blob/6c9236fd3b6a8f9e2d70dbf1bc01529242b73075/buffpy/managers/updates.py#L79-L99 | [
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... | 6c9236fd3b6a8f9e2d70dbf1bc01529242b73075 |
valid | Updates.new | Create one or more new status updates. | buffpy/managers/updates.py | def new(self, text, shorten=None, now=None, top=None, media=None, when=None):
'''
Create one or more new status updates.
'''
url = PATHS['CREATE']
post_data = "text=%s&" % text
post_data += "profile_ids[]=%s&" % self.profile_id
if shorten:
post_data += "shorten=%s&" % shorten
... | def new(self, text, shorten=None, now=None, top=None, media=None, when=None):
'''
Create one or more new status updates.
'''
url = PATHS['CREATE']
post_data = "text=%s&" % text
post_data += "profile_ids[]=%s&" % self.profile_id
if shorten:
post_data += "shorten=%s&" % shorten
... | [
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"."
] | vtemian/buffpy | python | https://github.com/vtemian/buffpy/blob/6c9236fd3b6a8f9e2d70dbf1bc01529242b73075/buffpy/managers/updates.py#L102-L135 | [
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"... | 6c9236fd3b6a8f9e2d70dbf1bc01529242b73075 |
valid | Logger.set_level | Set the logging level (which types of logs are actually printed / recorded)
to one of ['debug', 'info', 'warn', 'error', 'fatal'] in that order
of severity | peri/logger.py | def set_level(self, level='info', handlers=None):
"""
Set the logging level (which types of logs are actually printed / recorded)
to one of ['debug', 'info', 'warn', 'error', 'fatal'] in that order
of severity
"""
for h in self.get_handlers(handlers):
h.setLev... | def set_level(self, level='info', handlers=None):
"""
Set the logging level (which types of logs are actually printed / recorded)
to one of ['debug', 'info', 'warn', 'error', 'fatal'] in that order
of severity
"""
for h in self.get_handlers(handlers):
h.setLev... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/logger.py#L73-L80 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Logger.set_formatter | Set the text format of messages to one of the pre-determined forms,
one of ['quiet', 'minimal', 'standard', 'verbose'] | peri/logger.py | def set_formatter(self, formatter='standard', handlers=None):
"""
Set the text format of messages to one of the pre-determined forms,
one of ['quiet', 'minimal', 'standard', 'verbose']
"""
for h in self.get_handlers(handlers):
h.setFormatter(logging.Formatter(formatte... | def set_formatter(self, formatter='standard', handlers=None):
"""
Set the text format of messages to one of the pre-determined forms,
one of ['quiet', 'minimal', 'standard', 'verbose']
"""
for h in self.get_handlers(handlers):
h.setFormatter(logging.Formatter(formatte... | [
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valid | Logger.add_handler | Add another handler to the logging system if not present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log'] | peri/logger.py | def add_handler(self, name='console-color', level='info', formatter='standard', **kwargs):
"""
Add another handler to the logging system if not present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log']
"""
# make sure the the log file has ... | def add_handler(self, name='console-color', level='info', formatter='standard', **kwargs):
"""
Add another handler to the logging system if not present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log']
"""
# make sure the the log file has ... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/logger.py#L90-L104 | [
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valid | Logger.remove_handler | Remove handler from the logging system if present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log'] | peri/logger.py | def remove_handler(self, name):
"""
Remove handler from the logging system if present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log']
"""
if name in self.handlers:
self.log.removeHandler(self.handlers[name]) | def remove_handler(self, name):
"""
Remove handler from the logging system if present already.
Available handlers are currently: ['console-bw', 'console-color', 'rotating-log']
"""
if name in self.handlers:
self.log.removeHandler(self.handlers[name]) | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Logger.noformat | Temporarily do not use any formatter so that text printed is raw | peri/logger.py | def noformat(self):
""" Temporarily do not use any formatter so that text printed is raw """
try:
formats = {}
for h in self.get_handlers():
formats[h] = h.formatter
self.set_formatter(formatter='quiet')
yield
except Exception as e:... | def noformat(self):
""" Temporarily do not use any formatter so that text printed is raw """
try:
formats = {}
for h in self.get_handlers():
formats[h] = h.formatter
self.set_formatter(formatter='quiet')
yield
except Exception as e:... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/logger.py#L124-L136 | [
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"=",... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Logger.set_verbosity | Set the verbosity level of a certain log handler or of all handlers.
Parameters
----------
verbosity : 'v' to 'vvvvv'
the level of verbosity, more v's is more verbose
handlers : string, or list of strings
handler names can be found in ``peri.logger.types.keys()`... | peri/logger.py | def set_verbosity(self, verbosity='vvv', handlers=None):
"""
Set the verbosity level of a certain log handler or of all handlers.
Parameters
----------
verbosity : 'v' to 'vvvvv'
the level of verbosity, more v's is more verbose
handlers : string, or list of ... | def set_verbosity(self, verbosity='vvv', handlers=None):
"""
Set the verbosity level of a certain log handler or of all handlers.
Parameters
----------
verbosity : 'v' to 'vvvvv'
the level of verbosity, more v's is more verbose
handlers : string, or list of ... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/logger.py#L138-L155 | [
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valid | normalize | Normalize a field to a (min, max) exposure range, default is (0, 255).
(min, max) exposure values. Invert the image if requested. | peri/initializers.py | def normalize(im, invert=False, scale=None, dtype=np.float64):
"""
Normalize a field to a (min, max) exposure range, default is (0, 255).
(min, max) exposure values. Invert the image if requested.
"""
if dtype not in {np.float16, np.float32, np.float64}:
raise ValueError('dtype must be numpy... | def normalize(im, invert=False, scale=None, dtype=np.float64):
"""
Normalize a field to a (min, max) exposure range, default is (0, 255).
(min, max) exposure values. Invert the image if requested.
"""
if dtype not in {np.float16, np.float32, np.float64}:
raise ValueError('dtype must be numpy... | [
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valid | generate_sphere | Generates a centered boolean mask of a 3D sphere | peri/initializers.py | def generate_sphere(radius):
"""Generates a centered boolean mask of a 3D sphere"""
rint = np.ceil(radius).astype('int')
t = np.arange(-rint, rint+1, 1)
x,y,z = np.meshgrid(t, t, t, indexing='ij')
r = np.sqrt(x*x + y*y + z*z)
sphere = r < radius
return sphere | def generate_sphere(radius):
"""Generates a centered boolean mask of a 3D sphere"""
rint = np.ceil(radius).astype('int')
t = np.arange(-rint, rint+1, 1)
x,y,z = np.meshgrid(t, t, t, indexing='ij')
r = np.sqrt(x*x + y*y + z*z)
sphere = r < radius
return sphere | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/initializers.py#L81-L88 | [
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valid | local_max_featuring | Local max featuring to identify bright spherical particles on a
dark background.
Parameters
----------
im : numpy.ndarray
The image to identify particles in.
radius : Float > 0, optional
Featuring radius of the particles. Default is 2.5
noise_size : Float, op... | peri/initializers.py | def local_max_featuring(im, radius=2.5, noise_size=1., bkg_size=None,
minmass=1., trim_edge=False):
"""Local max featuring to identify bright spherical particles on a
dark background.
Parameters
----------
im : numpy.ndarray
The image to identify particles in.
radius... | def local_max_featuring(im, radius=2.5, noise_size=1., bkg_size=None,
minmass=1., trim_edge=False):
"""Local max featuring to identify bright spherical particles on a
dark background.
Parameters
----------
im : numpy.ndarray
The image to identify particles in.
radius... | [
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valid | otsu_threshold | Otsu threshold on data.
Otsu thresholding [1]_is a method for selecting an intensity value
for thresholding an image into foreground and background. The sel-
ected intensity threshold maximizes the inter-class variance.
Parameters
----------
data : numpy.ndarray
The data to thr... | peri/initializers.py | def otsu_threshold(data, bins=255):
"""
Otsu threshold on data.
Otsu thresholding [1]_is a method for selecting an intensity value
for thresholding an image into foreground and background. The sel-
ected intensity threshold maximizes the inter-class variance.
Parameters
----------
... | def otsu_threshold(data, bins=255):
"""
Otsu threshold on data.
Otsu thresholding [1]_is a method for selecting an intensity value
for thresholding an image into foreground and background. The sel-
ected intensity threshold maximizes the inter-class variance.
Parameters
----------
... | [
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valid | harris_feature | Harris-motivated feature detection on a d-dimensional image.
Parameters
---------
im
region_size
to_return : {'harris','matrix','trace-determinant'} | peri/initializers.py | def harris_feature(im, region_size=5, to_return='harris', scale=0.05):
"""
Harris-motivated feature detection on a d-dimensional image.
Parameters
---------
im
region_size
to_return : {'harris','matrix','trace-determinant'}
"""
ndim = im.ndim
#1. Gradient of image
... | def harris_feature(im, region_size=5, to_return='harris', scale=0.05):
"""
Harris-motivated feature detection on a d-dimensional image.
Parameters
---------
im
region_size
to_return : {'harris','matrix','trace-determinant'}
"""
ndim = im.ndim
#1. Gradient of image
... | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | identify_slab | Identifies slabs in an image.
Functions by running a Harris-inspired edge detection on the image,
thresholding the edge, then clustering.
Parameters
----------
im : numpy.ndarray
3D array of the image to analyze.
sigma : Float, optional
Gaussian blurring kernel ... | peri/initializers.py | def identify_slab(im, sigma=5., region_size=10, masscut=1e4, asdict=False):
"""
Identifies slabs in an image.
Functions by running a Harris-inspired edge detection on the image,
thresholding the edge, then clustering.
Parameters
----------
im : numpy.ndarray
3D array of the... | def identify_slab(im, sigma=5., region_size=10, masscut=1e4, asdict=False):
"""
Identifies slabs in an image.
Functions by running a Harris-inspired edge detection on the image,
thresholding the edge, then clustering.
Parameters
----------
im : numpy.ndarray
3D array of the... | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | plot_errors_single | ax = fig.add_axes([0.6, 0.6, 0.28, 0.28])
ax.plot(rad, crb[:,0,:], lw=2.5)
for c, error in enumerate(errors):
mu = np.sqrt((error**2).mean(axis=1))[:,0,:]
std = np.std(np.sqrt((error**2)), axis=1)[:,0,:]
for i in range(len(mu[0])):
ax.errorbar(rad, mu[:,i], yerr=std[:,i], fm... | scripts/quick_bench.py | def plot_errors_single(rad, crb, errors, labels=['trackpy', 'peri']):
fig = pl.figure()
comps = ['z', 'y', 'x']
markers = ['o', '^', '*']
colors = COLORS
for i in reversed(range(3)):
pl.plot(rad, crb[:,0,i], lw=2.5, label='CRB-'+comps[i], color=colors[i])
for c, (error, label) in enume... | def plot_errors_single(rad, crb, errors, labels=['trackpy', 'peri']):
fig = pl.figure()
comps = ['z', 'y', 'x']
markers = ['o', '^', '*']
colors = COLORS
for i in reversed(range(3)):
pl.plot(rad, crb[:,0,i], lw=2.5, label='CRB-'+comps[i], color=colors[i])
for c, (error, label) in enume... | [
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valid | sphere_triangle_cdf | Cumulative distribution function for the traingle distribution | peri/comp/objs.py | def sphere_triangle_cdf(dr, a, alpha):
""" Cumulative distribution function for the traingle distribution """
p0 = (dr+alpha)**2/(2*alpha**2)*(0 > dr)*(dr>-alpha)
p1 = 1*(dr>0)-(alpha-dr)**2/(2*alpha**2)*(0<dr)*(dr<alpha)
return (1-np.clip(p0+p1, 0, 1)) | def sphere_triangle_cdf(dr, a, alpha):
""" Cumulative distribution function for the traingle distribution """
p0 = (dr+alpha)**2/(2*alpha**2)*(0 > dr)*(dr>-alpha)
p1 = 1*(dr>0)-(alpha-dr)**2/(2*alpha**2)*(0<dr)*(dr<alpha)
return (1-np.clip(p0+p1, 0, 1)) | [
"Cumulative",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L315-L319 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | sphere_analytical_gaussian | Analytically calculate the sphere's functional form by convolving the
Heavyside function with first order approximation to the sinc, a Gaussian.
The alpha parameters controls the width of the approximation -- should be
1, but is fit to be roughly 0.2765 | peri/comp/objs.py | def sphere_analytical_gaussian(dr, a, alpha=0.2765):
"""
Analytically calculate the sphere's functional form by convolving the
Heavyside function with first order approximation to the sinc, a Gaussian.
The alpha parameters controls the width of the approximation -- should be
1, but is fit to be roug... | def sphere_analytical_gaussian(dr, a, alpha=0.2765):
"""
Analytically calculate the sphere's functional form by convolving the
Heavyside function with first order approximation to the sinc, a Gaussian.
The alpha parameters controls the width of the approximation -- should be
1, but is fit to be roug... | [
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valid | sphere_analytical_gaussian_trim | See sphere_analytical_gaussian_exact.
I trimmed to terms from the functional form that are essentially zero (1e-8)
for r0 > cut (~1.5), a fine approximation for these platonic anyway. | peri/comp/objs.py | def sphere_analytical_gaussian_trim(dr, a, alpha=0.2765, cut=1.6):
"""
See sphere_analytical_gaussian_exact.
I trimmed to terms from the functional form that are essentially zero (1e-8)
for r0 > cut (~1.5), a fine approximation for these platonic anyway.
"""
m = np.abs(dr) <= cut
# only co... | def sphere_analytical_gaussian_trim(dr, a, alpha=0.2765, cut=1.6):
"""
See sphere_analytical_gaussian_exact.
I trimmed to terms from the functional form that are essentially zero (1e-8)
for r0 > cut (~1.5), a fine approximation for these platonic anyway.
"""
m = np.abs(dr) <= cut
# only co... | [
"See",
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"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L335-L354 | [
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valid | sphere_analytical_gaussian_fast | See sphere_analytical_gaussian_trim, but implemented in C with
fast erf and exp approximations found at
Abramowitz and Stegun: Handbook of Mathematical Functions
A Fast, Compact Approximation of the Exponential Function
The default cut 1.25 was chosen based on the accuracy of fast_erf | peri/comp/objs.py | def sphere_analytical_gaussian_fast(dr, a, alpha=0.2765, cut=1.20):
"""
See sphere_analytical_gaussian_trim, but implemented in C with
fast erf and exp approximations found at
Abramowitz and Stegun: Handbook of Mathematical Functions
A Fast, Compact Approximation of the Exponential Function
... | def sphere_analytical_gaussian_fast(dr, a, alpha=0.2765, cut=1.20):
"""
See sphere_analytical_gaussian_trim, but implemented in C with
fast erf and exp approximations found at
Abramowitz and Stegun: Handbook of Mathematical Functions
A Fast, Compact Approximation of the Exponential Function
... | [
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"Approximation... | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L356-L389 | [
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"\"\"\"\n double coeff1 = 1.0/(alpha*sqrt(2.0));\n double coeff2 = sqrt(0.5/pi)*alpha;\n\n for (int i=0; i<N; i++){\n double... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | sphere_constrained_cubic | Sphere generated by a cubic interpolant constrained to be (1,0) on
(r0-sqrt(3)/2, r0+sqrt(3)/2), the size of the cube in the (111) direction. | peri/comp/objs.py | def sphere_constrained_cubic(dr, a, alpha):
"""
Sphere generated by a cubic interpolant constrained to be (1,0) on
(r0-sqrt(3)/2, r0+sqrt(3)/2), the size of the cube in the (111) direction.
"""
sqrt3 = np.sqrt(3)
b_coeff = a*0.5/sqrt3*(1 - 0.6*sqrt3*alpha)/(0.15 + a*a)
rscl = np.clip(dr, -0... | def sphere_constrained_cubic(dr, a, alpha):
"""
Sphere generated by a cubic interpolant constrained to be (1,0) on
(r0-sqrt(3)/2, r0+sqrt(3)/2), the size of the cube in the (111) direction.
"""
sqrt3 = np.sqrt(3)
b_coeff = a*0.5/sqrt3*(1 - 0.6*sqrt3*alpha)/(0.15 + a*a)
rscl = np.clip(dr, -0... | [
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valid | exact_volume_sphere | Perform an iterative method to calculate the effective sphere that perfectly
(up to the volume_error) conserves volume. Return the resulting image | peri/comp/objs.py | def exact_volume_sphere(rvec, pos, radius, zscale=1.0, volume_error=1e-5,
function=sphere_analytical_gaussian, max_radius_change=1e-2, args=()):
"""
Perform an iterative method to calculate the effective sphere that perfectly
(up to the volume_error) conserves volume. Return the resulting image
... | def exact_volume_sphere(rvec, pos, radius, zscale=1.0, volume_error=1e-5,
function=sphere_analytical_gaussian, max_radius_change=1e-2, args=()):
"""
Perform an iterative method to calculate the effective sphere that perfectly
(up to the volume_error) conserves volume. Return the resulting image
... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L409-L433 | [
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"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicParticlesCollection._tile | Get the update tile surrounding particle `n` | peri/comp/objs.py | def _tile(self, n):
"""Get the update tile surrounding particle `n` """
pos = self._trans(self.pos[n])
return Tile(pos, pos).pad(self.support_pad) | def _tile(self, n):
"""Get the update tile surrounding particle `n` """
pos = self._trans(self.pos[n])
return Tile(pos, pos).pad(self.support_pad) | [
"Get",
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"surrounding",
"particle",
"n"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L160-L163 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicParticlesCollection._p2i | Parameter to indices, returns (coord, index), e.g. for a pos
pos : ('x', 100) | peri/comp/objs.py | def _p2i(self, param):
"""
Parameter to indices, returns (coord, index), e.g. for a pos
pos : ('x', 100)
"""
g = param.split('-')
if len(g) == 3:
return g[2], int(g[1])
else:
raise ValueError('`param` passed as incorrect format') | def _p2i(self, param):
"""
Parameter to indices, returns (coord, index), e.g. for a pos
pos : ('x', 100)
"""
g = param.split('-')
if len(g) == 3:
return g[2], int(g[1])
else:
raise ValueError('`param` passed as incorrect format') | [
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"pos",
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valid | PlatonicParticlesCollection.initialize | Start from scratch and initialize all objects / draw self.particles | peri/comp/objs.py | def initialize(self):
"""Start from scratch and initialize all objects / draw self.particles"""
self.particles = np.zeros(self.shape.shape, dtype=self.float_precision)
for p0, arg0 in zip(self.pos, self._drawargs()):
self._draw_particle(p0, *listify(arg0)) | def initialize(self):
"""Start from scratch and initialize all objects / draw self.particles"""
self.particles = np.zeros(self.shape.shape, dtype=self.float_precision)
for p0, arg0 in zip(self.pos, self._drawargs()):
self._draw_particle(p0, *listify(arg0)) | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L186-L191 | [
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valid | PlatonicParticlesCollection._vps | Clips a list of inds to be on [0, self.N] | peri/comp/objs.py | def _vps(self, inds):
"""Clips a list of inds to be on [0, self.N]"""
return [j for j in inds if j >= 0 and j < self.N] | def _vps(self, inds):
"""Clips a list of inds to be on [0, self.N]"""
return [j for j in inds if j >= 0 and j < self.N] | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L200-L202 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicParticlesCollection._i2p | Translate index info to parameter name | peri/comp/objs.py | def _i2p(self, ind, coord):
""" Translate index info to parameter name """
return '-'.join([self.param_prefix, str(ind), coord]) | def _i2p(self, ind, coord):
""" Translate index info to parameter name """
return '-'.join([self.param_prefix, str(ind), coord]) | [
"Translate",
"index",
"info",
"to",
"parameter",
"name"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L232-L234 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicParticlesCollection.get_update_tile | Get the amount of support size required for a particular update. | peri/comp/objs.py | def get_update_tile(self, params, values):
""" Get the amount of support size required for a particular update."""
doglobal, particles = self._update_type(params)
if doglobal:
return self.shape.copy()
# 1) store the current parameters of interest
values0 = self.get_v... | def get_update_tile(self, params, values):
""" Get the amount of support size required for a particular update."""
doglobal, particles = self._update_type(params)
if doglobal:
return self.shape.copy()
# 1) store the current parameters of interest
values0 = self.get_v... | [
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valid | PlatonicParticlesCollection.update | Update the particles field given new parameter values | peri/comp/objs.py | def update(self, params, values):
"""
Update the particles field given new parameter values
"""
#1. Figure out if we're going to do a global update, in which
# case we just draw from scratch.
global_update, particles = self._update_type(params)
# if we are doin... | def update(self, params, values):
"""
Update the particles field given new parameter values
"""
#1. Figure out if we're going to do a global update, in which
# case we just draw from scratch.
global_update, particles = self._update_type(params)
# if we are doin... | [
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"# if we ... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicSpheresCollection.param_particle | Get position and radius of one or more particles | peri/comp/objs.py | def param_particle(self, ind):
""" Get position and radius of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, j) for i in ind for j in ['z', 'y', 'x', 'a']] | def param_particle(self, ind):
""" Get position and radius of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, j) for i in ind for j in ['z', 'y', 'x', 'a']] | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L647-L650 | [
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valid | PlatonicSpheresCollection.param_particle_pos | Get position of one or more particles | peri/comp/objs.py | def param_particle_pos(self, ind):
""" Get position of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, j) for i in ind for j in ['z', 'y', 'x']] | def param_particle_pos(self, ind):
""" Get position of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, j) for i in ind for j in ['z', 'y', 'x']] | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L652-L655 | [
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valid | PlatonicSpheresCollection.param_particle_rad | Get radius of one or more particles | peri/comp/objs.py | def param_particle_rad(self, ind):
""" Get radius of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, 'a') for i in ind] | def param_particle_rad(self, ind):
""" Get radius of one or more particles """
ind = self._vps(listify(ind))
return [self._i2p(i, 'a') for i in ind] | [
"Get",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L657-L660 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicSpheresCollection.add_particle | Add a particle or list of particles given by a list of positions and
radii, both need to be array-like.
Parameters
----------
pos : array-like [N, 3]
Positions of all new particles
rad : array-like [N]
Corresponding radii of new particles
Return... | peri/comp/objs.py | def add_particle(self, pos, rad):
"""
Add a particle or list of particles given by a list of positions and
radii, both need to be array-like.
Parameters
----------
pos : array-like [N, 3]
Positions of all new particles
rad : array-like [N]
... | def add_particle(self, pos, rad):
"""
Add a particle or list of particles given by a list of positions and
radii, both need to be array-like.
Parameters
----------
pos : array-like [N, 3]
Positions of all new particles
rad : array-like [N]
... | [
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"-",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L662-L694 | [
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"arange... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicSpheresCollection.remove_particle | Remove the particle at index `inds`, may be a list.
Returns [3,N], [N] element numpy.ndarray of pos, rad. | peri/comp/objs.py | def remove_particle(self, inds):
"""
Remove the particle at index `inds`, may be a list.
Returns [3,N], [N] element numpy.ndarray of pos, rad.
"""
if self.rad.shape[0] == 0:
return
inds = listify(inds)
# Here's the game plan:
# 1. get all p... | def remove_particle(self, inds):
"""
Remove the particle at index `inds`, may be a list.
Returns [3,N], [N] element numpy.ndarray of pos, rad.
"""
if self.rad.shape[0] == 0:
return
inds = listify(inds)
# Here's the game plan:
# 1. get all p... | [
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"# 1. get all positions and sizes of particles... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | PlatonicSpheresCollection._update_type | Returns dozscale and particle list of update | peri/comp/objs.py | def _update_type(self, params):
""" Returns dozscale and particle list of update """
dozscale = False
particles = []
for p in listify(params):
typ, ind = self._p2i(p)
particles.append(ind)
dozscale = dozscale or typ == 'zscale'
particles = set(... | def _update_type(self, params):
""" Returns dozscale and particle list of update """
dozscale = False
particles = []
for p in listify(params):
typ, ind = self._p2i(p)
particles.append(ind)
dozscale = dozscale or typ == 'zscale'
particles = set(... | [
"Returns",
"dozscale",
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"list",
"of",
"update"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L746-L755 | [
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valid | PlatonicSpheresCollection._tile | Get the tile surrounding particle `n` | peri/comp/objs.py | def _tile(self, n):
""" Get the tile surrounding particle `n` """
zsc = np.array([1.0/self.zscale, 1, 1])
pos, rad = self.pos[n], self.rad[n]
pos = self._trans(pos)
return Tile(pos - zsc*rad, pos + zsc*rad).pad(self.support_pad) | def _tile(self, n):
""" Get the tile surrounding particle `n` """
zsc = np.array([1.0/self.zscale, 1, 1])
pos, rad = self.pos[n], self.rad[n]
pos = self._trans(pos)
return Tile(pos - zsc*rad, pos + zsc*rad).pad(self.support_pad) | [
"Get",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L757-L762 | [
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valid | PlatonicSpheresCollection.update | Calls an update, but clips radii to be > 0 | peri/comp/objs.py | def update(self, params, values):
"""Calls an update, but clips radii to be > 0"""
# radparams = self.param_radii()
params = listify(params)
values = listify(values)
for i, p in enumerate(params):
# if (p in radparams) & (values[i] < 0):
if (p[-2:] == '-a'... | def update(self, params, values):
"""Calls an update, but clips radii to be > 0"""
# radparams = self.param_radii()
params = listify(params)
values = listify(values)
for i, p in enumerate(params):
# if (p in radparams) & (values[i] < 0):
if (p[-2:] == '-a'... | [
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"0"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L764-L773 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Slab.rmatrix | Generate the composite rotation matrix that rotates the slab normal.
The rotation is a rotation about the x-axis, followed by a rotation
about the z-axis. | peri/comp/objs.py | def rmatrix(self):
"""
Generate the composite rotation matrix that rotates the slab normal.
The rotation is a rotation about the x-axis, followed by a rotation
about the z-axis.
"""
t = self.param_dict[self.lbl_theta]
r0 = np.array([ [np.cos(t), -np.sin(t), 0],
... | def rmatrix(self):
"""
Generate the composite rotation matrix that rotates the slab normal.
The rotation is a rotation about the x-axis, followed by a rotation
about the z-axis.
"""
t = self.param_dict[self.lbl_theta]
r0 = np.array([ [np.cos(t), -np.sin(t), 0],
... | [
"Generate",
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"normal",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/objs.py#L848-L864 | [
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valid | j2 | A fast j2 defined in terms of other special functions | peri/comp/psfcalc.py | def j2(x):
""" A fast j2 defined in terms of other special functions """
to_return = 2./(x+1e-15)*j1(x) - j0(x)
to_return[x==0] = 0
return to_return | def j2(x):
""" A fast j2 defined in terms of other special functions """
to_return = 2./(x+1e-15)*j1(x) - j0(x)
to_return[x==0] = 0
return to_return | [
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"special",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L12-L16 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calc_pts_hg | Returns Hermite-Gauss quadrature points for even functions | peri/comp/psfcalc.py | def calc_pts_hg(npts=20):
"""Returns Hermite-Gauss quadrature points for even functions"""
pts_hg, wts_hg = np.polynomial.hermite.hermgauss(npts*2)
pts_hg = pts_hg[npts:]
wts_hg = wts_hg[npts:] * np.exp(pts_hg*pts_hg)
return pts_hg, wts_hg | def calc_pts_hg(npts=20):
"""Returns Hermite-Gauss quadrature points for even functions"""
pts_hg, wts_hg = np.polynomial.hermite.hermgauss(npts*2)
pts_hg = pts_hg[npts:]
wts_hg = wts_hg[npts:] * np.exp(pts_hg*pts_hg)
return pts_hg, wts_hg | [
"Returns",
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"for",
"even",
"functions"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L20-L25 | [
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valid | calc_pts_lag | Returns Gauss-Laguerre quadrature points rescaled for line scan integration
Parameters
----------
npts : {15, 20, 25}, optional
The number of points to
Notes
-----
The scale is set internally as the best rescaling for a line scan
integral; it was checked numerically... | peri/comp/psfcalc.py | def calc_pts_lag(npts=20):
"""
Returns Gauss-Laguerre quadrature points rescaled for line scan integration
Parameters
----------
npts : {15, 20, 25}, optional
The number of points to
Notes
-----
The scale is set internally as the best rescaling for a line scan
... | def calc_pts_lag(npts=20):
"""
Returns Gauss-Laguerre quadrature points rescaled for line scan integration
Parameters
----------
npts : {15, 20, 25}, optional
The number of points to
Notes
-----
The scale is set internally as the best rescaling for a line scan
... | [
"Returns",
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"-",
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"quadrature",
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"rescaled",
"for",
"line",
"scan",
"integration"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L27-L55 | [
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valid | f_theta | Returns the wavefront aberration for an aberrated, defocused lens.
Calculates the portions of the wavefront distortion due to z, theta
only, for a lens with defocus and spherical aberration induced by
coverslip mismatch. (The rho portion can be analytically integrated
to Bessels.)
Parameters
-... | peri/comp/psfcalc.py | def f_theta(cos_theta, zint, z, n2n1=0.95, sph6_ab=None, **kwargs):
"""
Returns the wavefront aberration for an aberrated, defocused lens.
Calculates the portions of the wavefront distortion due to z, theta
only, for a lens with defocus and spherical aberration induced by
coverslip mismatch. (The r... | def f_theta(cos_theta, zint, z, n2n1=0.95, sph6_ab=None, **kwargs):
"""
Returns the wavefront aberration for an aberrated, defocused lens.
Calculates the portions of the wavefront distortion due to z, theta
only, for a lens with defocus and spherical aberration induced by
coverslip mismatch. (The r... | [
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"wavefront",
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"defocused",
"lens",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L61-L101 | [
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"zint... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_Kprefactor | Returns a prefactor in the electric field integral.
This is an internal function called by get_K. The returned prefactor
in the integrand is independent of which integral is being called;
it is a combination of the exp(1j*phase) and apodization.
Parameters
----------
z : numpy.ndarray
... | peri/comp/psfcalc.py | def get_Kprefactor(z, cos_theta, zint=100.0, n2n1=0.95, get_hdet=False,
**kwargs):
"""
Returns a prefactor in the electric field integral.
This is an internal function called by get_K. The returned prefactor
in the integrand is independent of which integral is being called;
it is a combinat... | def get_Kprefactor(z, cos_theta, zint=100.0, n2n1=0.95, get_hdet=False,
**kwargs):
"""
Returns a prefactor in the electric field integral.
This is an internal function called by get_K. The returned prefactor
in the integrand is independent of which integral is being called;
it is a combinat... | [
"Returns",
"a",
"prefactor",
"in",
"the",
"electric",
"field",
"integral",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L145-L186 | [
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valid | get_K | Calculates one of three electric field integrals.
Internal function for calculating point spread functions. Returns
one of three electric field integrals that describe the electric
field near the focus of a lens; these integrals appear in Hell's psf
calculation.
Parameters
----------
r... | peri/comp/psfcalc.py | def get_K(rho, z, alpha=1.0, zint=100.0, n2n1=0.95, get_hdet=False, K=1,
Kprefactor=None, return_Kprefactor=False, npts=20, **kwargs):
"""
Calculates one of three electric field integrals.
Internal function for calculating point spread functions. Returns
one of three electric field integrals th... | def get_K(rho, z, alpha=1.0, zint=100.0, n2n1=0.95, get_hdet=False, K=1,
Kprefactor=None, return_Kprefactor=False, npts=20, **kwargs):
"""
Calculates one of three electric field integrals.
Internal function for calculating point spread functions. Returns
one of three electric field integrals th... | [
"Calculates",
"one",
"of",
"three",
"electric",
"field",
"integrals",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L188-L294 | [
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"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_hsym_asym | Calculates the symmetric and asymmetric portions of a confocal PSF.
Parameters
----------
rho : numpy.ndarray
Rho in cylindrical coordinates, in units of 1/k.
z : numpy.ndarray
Z in cylindrical coordinates, in units of 1/k. Must be the
same shape as `rho`
... | peri/comp/psfcalc.py | def get_hsym_asym(rho, z, get_hdet=False, include_K3_det=True, **kwargs):
"""
Calculates the symmetric and asymmetric portions of a confocal PSF.
Parameters
----------
rho : numpy.ndarray
Rho in cylindrical coordinates, in units of 1/k.
z : numpy.ndarray
Z in cyl... | def get_hsym_asym(rho, z, get_hdet=False, include_K3_det=True, **kwargs):
"""
Calculates the symmetric and asymmetric portions of a confocal PSF.
Parameters
----------
rho : numpy.ndarray
Rho in cylindrical coordinates, in units of 1/k.
z : numpy.ndarray
Z in cyl... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L300-L355 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calculate_pinhole_psf | Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PSF in units of 1/ the wavevector of
the incoming light.
y : numpy.ndarray
The y-coordinate.
z : numpy.ndarray
... | peri/comp/psfcalc.py | def calculate_pinhole_psf(x, y, z, kfki=0.89, zint=100.0, normalize=False,
**kwargs):
"""
Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PSF in units of 1/ the wavevector of
the in... | def calculate_pinhole_psf(x, y, z, kfki=0.89, zint=100.0, normalize=False,
**kwargs):
"""
Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PSF in units of 1/ the wavevector of
the in... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L357-L419 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_polydisp_pts_wts | Calculates a set of Gauss quadrature points & weights for polydisperse
light.
Returns a list of points and weights of the final wavevector's distri-
bution, in units of the initial wavevector.
Parameters
----------
kfki : Float
The mean of the polydisperse outgoing wavevectors.... | peri/comp/psfcalc.py | def get_polydisp_pts_wts(kfki, sigkf, dist_type='gaussian', nkpts=3):
"""
Calculates a set of Gauss quadrature points & weights for polydisperse
light.
Returns a list of points and weights of the final wavevector's distri-
bution, in units of the initial wavevector.
Parameters
----------
... | def get_polydisp_pts_wts(kfki, sigkf, dist_type='gaussian', nkpts=3):
"""
Calculates a set of Gauss quadrature points & weights for polydisperse
light.
Returns a list of points and weights of the final wavevector's distri-
bution, in units of the initial wavevector.
Parameters
----------
... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L421-L462 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calculate_polychrome_pinhole_psf | Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PSF in units of 1/ the wavevector of
the incoming light.
y : numpy.ndarray
The y-coordinate.
z : numpy.ndarray
... | peri/comp/psfcalc.py | def calculate_polychrome_pinhole_psf(x, y, z, normalize=False, kfki=0.889,
sigkf=0.1, zint=100., nkpts=3, dist_type='gaussian', **kwargs):
"""
Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PS... | def calculate_polychrome_pinhole_psf(x, y, z, normalize=False, kfki=0.889,
sigkf=0.1, zint=100., nkpts=3, dist_type='gaussian', **kwargs):
"""
Calculates the perfect-pinhole PSF, for a set of points (x,y,z).
Parameters
-----------
x : numpy.ndarray
The x-coordinate of the PS... | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_psf_scalar | Calculates a scalar (non-vectorial light) approximation to a confocal PSF
The calculation is approximate, since it ignores the effects of
polarization and apodization, but should be ~3x faster.
Parameters
----------
x : numpy.ndarray
The x-coordinate of the PSF in units of 1/ the w... | peri/comp/psfcalc.py | def get_psf_scalar(x, y, z, kfki=1., zint=100.0, normalize=False, **kwargs):
"""
Calculates a scalar (non-vectorial light) approximation to a confocal PSF
The calculation is approximate, since it ignores the effects of
polarization and apodization, but should be ~3x faster.
Parameters
--------... | def get_psf_scalar(x, y, z, kfki=1., zint=100.0, normalize=False, **kwargs):
"""
Calculates a scalar (non-vectorial light) approximation to a confocal PSF
The calculation is approximate, since it ignores the effects of
polarization and apodization, but should be ~3x faster.
Parameters
--------... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L545-L618 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calculate_linescan_ilm_psf | Calculates the illumination PSF for a line-scanning confocal with the
confocal line oriented along the x direction.
Parameters
----------
y : numpy.ndarray
The y points (in-plane, perpendicular to the line direction)
at which to evaluate the illumination PSF, in units of 1/k... | peri/comp/psfcalc.py | def calculate_linescan_ilm_psf(y,z, polar_angle=0., nlpts=1,
pinhole_width=1, use_laggauss=False, **kwargs):
"""
Calculates the illumination PSF for a line-scanning confocal with the
confocal line oriented along the x direction.
Parameters
----------
y : numpy.ndarray
Th... | def calculate_linescan_ilm_psf(y,z, polar_angle=0., nlpts=1,
pinhole_width=1, use_laggauss=False, **kwargs):
"""
Calculates the illumination PSF for a line-scanning confocal with the
confocal line oriented along the x direction.
Parameters
----------
y : numpy.ndarray
Th... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L620-L700 | [
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"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calculate_linescan_psf | Calculates the point spread function of a line-scanning confocal.
Make x,y,z __1D__ numpy.arrays, with x the direction along the
scan line. (to make the calculation faster since I dont' need the line
ilm for each x).
Parameters
----------
x : numpy.ndarray
_One_dimensional_ ar... | peri/comp/psfcalc.py | def calculate_linescan_psf(x, y, z, normalize=False, kfki=0.889, zint=100.,
polar_angle=0., wrap=True, **kwargs):
"""
Calculates the point spread function of a line-scanning confocal.
Make x,y,z __1D__ numpy.arrays, with x the direction along the
scan line. (to make the calculation faster sinc... | def calculate_linescan_psf(x, y, z, normalize=False, kfki=0.889, zint=100.,
polar_angle=0., wrap=True, **kwargs):
"""
Calculates the point spread function of a line-scanning confocal.
Make x,y,z __1D__ numpy.arrays, with x the direction along the
scan line. (to make the calculation faster sinc... | [
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"line",
"-",
"scanning",
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"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L702-L797 | [
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"#0. Set... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | calculate_polychrome_linescan_psf | Calculates the point spread function of a line-scanning confocal with
polydisperse dye emission.
Make x,y,z __1D__ numpy.arrays, with x the direction along the
scan line. (to make the calculation faster since I dont' need the line
ilm for each x).
Parameters
----------
x : numpy.ndarr... | peri/comp/psfcalc.py | def calculate_polychrome_linescan_psf(x, y, z, normalize=False, kfki=0.889,
sigkf=0.1, zint=100., nkpts=3, dist_type='gaussian', wrap=True,
**kwargs):
"""
Calculates the point spread function of a line-scanning confocal with
polydisperse dye emission.
Make x,y,z __1D__ numpy.arrays, wi... | def calculate_polychrome_linescan_psf(x, y, z, normalize=False, kfki=0.889,
sigkf=0.1, zint=100., nkpts=3, dist_type='gaussian', wrap=True,
**kwargs):
"""
Calculates the point spread function of a line-scanning confocal with
polydisperse dye emission.
Make x,y,z __1D__ numpy.arrays, wi... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L799-L913 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | wrap_and_calc_psf | Wraps a point-spread function in x and y.
Speeds up psf calculations by a factor of 4 for free / some broadcasting
by exploiting the x->-x, y->-y symmetry of a psf function. Pass x and y
as the positive (say) values of the coordinates at which to evaluate func,
and it will return the function sampled a... | peri/comp/psfcalc.py | def wrap_and_calc_psf(xpts, ypts, zpts, func, **kwargs):
"""
Wraps a point-spread function in x and y.
Speeds up psf calculations by a factor of 4 for free / some broadcasting
by exploiting the x->-x, y->-y symmetry of a psf function. Pass x and y
as the positive (say) values of the coordinates at ... | def wrap_and_calc_psf(xpts, ypts, zpts, func, **kwargs):
"""
Wraps a point-spread function in x and y.
Speeds up psf calculations by a factor of 4 for free / some broadcasting
by exploiting the x->-x, y->-y symmetry of a psf function. Pass x and y
as the positive (say) values of the coordinates at ... | [
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"-",
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"x",
"and",
"y",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/comp/psfcalc.py#L920-L992 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | vec_to_halfvec | Transforms a vector np.arange(-N, M, dx) to np.arange(min(|vec|), max(N,M),dx)] | peri/comp/psfcalc.py | def vec_to_halfvec(vec):
"""Transforms a vector np.arange(-N, M, dx) to np.arange(min(|vec|), max(N,M),dx)]"""
d = vec[1:] - vec[:-1]
if ((d/d.mean()).std() > 1e-14) or (d.mean() < 0):
raise ValueError('vec must be np.arange() in increasing order')
dx = d.mean()
lowest = np.abs(vec).min()
... | def vec_to_halfvec(vec):
"""Transforms a vector np.arange(-N, M, dx) to np.arange(min(|vec|), max(N,M),dx)]"""
d = vec[1:] - vec[:-1]
if ((d/d.mean()).std() > 1e-14) or (d.mean() < 0):
raise ValueError('vec must be np.arange() in increasing order')
dx = d.mean()
lowest = np.abs(vec).min()
... | [
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valid | listify | Convert a scalar ``a`` to a list and all iterables to list as well.
Examples
--------
>>> listify(0)
[0]
>>> listify([1,2,3])
[1, 2, 3]
>>> listify('a')
['a']
>>> listify(np.array([1,2,3]))
[1, 2, 3]
>>> listify('string')
['string'] | peri/util.py | def listify(a):
"""
Convert a scalar ``a`` to a list and all iterables to list as well.
Examples
--------
>>> listify(0)
[0]
>>> listify([1,2,3])
[1, 2, 3]
>>> listify('a')
['a']
>>> listify(np.array([1,2,3]))
[1, 2, 3]
>>> listify('string')
['string']
""... | def listify(a):
"""
Convert a scalar ``a`` to a list and all iterables to list as well.
Examples
--------
>>> listify(0)
[0]
>>> listify([1,2,3])
[1, 2, 3]
>>> listify('a')
['a']
>>> listify(np.array([1,2,3]))
[1, 2, 3]
>>> listify('string')
['string']
""... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L34-L59 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | delistify | If a single element list, extract the element as an object, otherwise
leave as it is.
Examples
--------
>>> delistify('string')
'string'
>>> delistify(['string'])
'string'
>>> delistify(['string', 'other'])
['string', 'other']
>>> delistify(np.array([1.0]))
1.0
>>> d... | peri/util.py | def delistify(a, b=None):
"""
If a single element list, extract the element as an object, otherwise
leave as it is.
Examples
--------
>>> delistify('string')
'string'
>>> delistify(['string'])
'string'
>>> delistify(['string', 'other'])
['string', 'other']
>>> delisti... | def delistify(a, b=None):
"""
If a single element list, extract the element as an object, otherwise
leave as it is.
Examples
--------
>>> delistify('string')
'string'
>>> delistify(['string'])
'string'
>>> delistify(['string', 'other'])
['string', 'other']
>>> delisti... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L61-L91 | [
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valid | aN | Convert an integer or iterable list to numpy array of length dim. This func
is used to allow other methods to take both scalars non-numpy arrays with
flexibility.
Parameters
----------
a : number, iterable, array-like
The object to convert to numpy array
dim : integer
The lengt... | peri/util.py | def aN(a, dim=3, dtype='int'):
"""
Convert an integer or iterable list to numpy array of length dim. This func
is used to allow other methods to take both scalars non-numpy arrays with
flexibility.
Parameters
----------
a : number, iterable, array-like
The object to convert to numpy... | def aN(a, dim=3, dtype='int'):
"""
Convert an integer or iterable list to numpy array of length dim. This func
is used to allow other methods to take both scalars non-numpy arrays with
flexibility.
Parameters
----------
a : number, iterable, array-like
The object to convert to numpy... | [
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valid | cdd | Conditionally delete key (or list of keys) 'k' from dict 'd' | peri/util.py | def cdd(d, k):
""" Conditionally delete key (or list of keys) 'k' from dict 'd' """
if not isinstance(k, list):
k = [k]
for i in k:
if i in d:
d.pop(i) | def cdd(d, k):
""" Conditionally delete key (or list of keys) 'k' from dict 'd' """
if not isinstance(k, list):
k = [k]
for i in k:
if i in d:
d.pop(i) | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L883-L889 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | patch_docs | Apply the documentation from ``superclass`` to ``subclass`` by filling
in all overridden member function docstrings with those from the
parent class | peri/util.py | def patch_docs(subclass, superclass):
"""
Apply the documentation from ``superclass`` to ``subclass`` by filling
in all overridden member function docstrings with those from the
parent class
"""
funcs0 = inspect.getmembers(subclass, predicate=inspect.ismethod)
funcs1 = inspect.getmembers(sup... | def patch_docs(subclass, superclass):
"""
Apply the documentation from ``superclass`` to ``subclass`` by filling
in all overridden member function docstrings with those from the
parent class
"""
funcs0 = inspect.getmembers(subclass, predicate=inspect.ismethod)
funcs1 = inspect.getmembers(sup... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L1119-L1139 | [
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valid | indir | Context manager for switching the current path of the process. Can be used:
with indir('/tmp'):
<do something in tmp> | peri/util.py | def indir(path):
"""
Context manager for switching the current path of the process. Can be used:
with indir('/tmp'):
<do something in tmp>
"""
cwd = os.getcwd()
try:
os.chdir(path)
yield
except Exception as e:
raise
finally:
os.chdir(cwd) | def indir(path):
"""
Context manager for switching the current path of the process. Can be used:
with indir('/tmp'):
<do something in tmp>
"""
cwd = os.getcwd()
try:
os.chdir(path)
yield
except Exception as e:
raise
finally:
os.chdir(cwd) | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L1145-L1160 | [
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valid | Tile.slicer | Array slicer object for this tile
>>> Tile((2,3)).slicer
(slice(0, 2, None), slice(0, 3, None))
>>> np.arange(10)[Tile((4,)).slicer]
array([0, 1, 2, 3]) | peri/util.py | def slicer(self):
"""
Array slicer object for this tile
>>> Tile((2,3)).slicer
(slice(0, 2, None), slice(0, 3, None))
>>> np.arange(10)[Tile((4,)).slicer]
array([0, 1, 2, 3])
"""
return tuple(np.s_[l:r] for l,r in zip(*self.bounds)) | def slicer(self):
"""
Array slicer object for this tile
>>> Tile((2,3)).slicer
(slice(0, 2, None), slice(0, 3, None))
>>> np.arange(10)[Tile((4,)).slicer]
array([0, 1, 2, 3])
"""
return tuple(np.s_[l:r] for l,r in zip(*self.bounds)) | [
"Array",
"slicer",
"object",
"for",
"this",
"tile"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L298-L308 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Tile.oslicer | Opposite slicer, the outer part wrt to a field | peri/util.py | def oslicer(self, tile):
""" Opposite slicer, the outer part wrt to a field """
mask = None
vecs = tile.coords(form='meshed')
for v in vecs:
v[self.slicer] = -1
mask = mask & (v > 0) if mask is not None else (v>0)
return tuple(np.array(i).astype('int') for... | def oslicer(self, tile):
""" Opposite slicer, the outer part wrt to a field """
mask = None
vecs = tile.coords(form='meshed')
for v in vecs:
v[self.slicer] = -1
mask = mask & (v > 0) if mask is not None else (v>0)
return tuple(np.array(i).astype('int') for... | [
"Opposite",
"slicer",
"the",
"outer",
"part",
"wrt",
"to",
"a",
"field"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L310-L317 | [
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valid | Tile.kcenter | Return the frequency center of the tile (says fftshift) | peri/util.py | def kcenter(self):
""" Return the frequency center of the tile (says fftshift) """
return np.array([
np.abs(np.fft.fftshift(np.fft.fftfreq(q))).argmin()
for q in self.shape
]).astype('float') | def kcenter(self):
""" Return the frequency center of the tile (says fftshift) """
return np.array([
np.abs(np.fft.fftshift(np.fft.fftfreq(q))).argmin()
for q in self.shape
]).astype('float') | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L351-L356 | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Tile.corners | Iterate the vector of all corners of the hyperrectangles
>>> Tile(3, dim=2).corners
array([[0, 0],
[0, 3],
[3, 0],
[3, 3]]) | peri/util.py | def corners(self):
"""
Iterate the vector of all corners of the hyperrectangles
>>> Tile(3, dim=2).corners
array([[0, 0],
[0, 3],
[3, 0],
[3, 3]])
"""
corners = []
for ind in itertools.product(*((0,1),)*self.dim):
... | def corners(self):
"""
Iterate the vector of all corners of the hyperrectangles
>>> Tile(3, dim=2).corners
array([[0, 0],
[0, 3],
[3, 0],
[3, 3]])
"""
corners = []
for ind in itertools.product(*((0,1),)*self.dim):
... | [
"Iterate",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L359-L373 | [
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valid | Tile._format_vector | Format a 3d vector field in certain ways, see `coords` for a description
of each formatting method. | peri/util.py | def _format_vector(self, vecs, form='broadcast'):
"""
Format a 3d vector field in certain ways, see `coords` for a description
of each formatting method.
"""
if form == 'meshed':
return np.meshgrid(*vecs, indexing='ij')
elif form == 'vector':
vecs ... | def _format_vector(self, vecs, form='broadcast'):
"""
Format a 3d vector field in certain ways, see `coords` for a description
of each formatting method.
"""
if form == 'meshed':
return np.meshgrid(*vecs, indexing='ij')
elif form == 'vector':
vecs ... | [
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valid | Tile.coords | Returns the coordinate vectors associated with the tile.
Parameters
-----------
norm : boolean
can rescale the coordinates for you. False is no rescaling, True is
rescaling so that all coordinates are from 0 -> 1. If a scalar,
the same norm is applied unifor... | peri/util.py | def coords(self, norm=False, form='broadcast'):
"""
Returns the coordinate vectors associated with the tile.
Parameters
-----------
norm : boolean
can rescale the coordinates for you. False is no rescaling, True is
rescaling so that all coordinates are fr... | def coords(self, norm=False, form='broadcast'):
"""
Returns the coordinate vectors associated with the tile.
Parameters
-----------
norm : boolean
can rescale the coordinates for you. False is no rescaling, True is
rescaling so that all coordinates are fr... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L390-L440 | [
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valid | Tile.kvectors | Return the kvectors associated with this tile, given the standard form
of -0.5 to 0.5. `norm` and `form` arguments arethe same as that passed to
`Tile.coords`.
Parameters
-----------
real : boolean
whether to return kvectors associated with the real fft instead | peri/util.py | def kvectors(self, norm=False, form='broadcast', real=False, shift=False):
"""
Return the kvectors associated with this tile, given the standard form
of -0.5 to 0.5. `norm` and `form` arguments arethe same as that passed to
`Tile.coords`.
Parameters
-----------
r... | def kvectors(self, norm=False, form='broadcast', real=False, shift=False):
"""
Return the kvectors associated with this tile, given the standard form
of -0.5 to 0.5. `norm` and `form` arguments arethe same as that passed to
`Tile.coords`.
Parameters
-----------
r... | [
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valid | Tile.contains | Test whether coordinates are contained within this tile.
Parameters
----------
items : ndarray [3] or [N, 3]
N coordinates to check are within the bounds of the tile
pad : integer or ndarray [3]
anisotropic padding to apply in the contain test
Examples
... | peri/util.py | def contains(self, items, pad=0):
"""
Test whether coordinates are contained within this tile.
Parameters
----------
items : ndarray [3] or [N, 3]
N coordinates to check are within the bounds of the tile
pad : integer or ndarray [3]
anisotropic p... | def contains(self, items, pad=0):
"""
Test whether coordinates are contained within this tile.
Parameters
----------
items : ndarray [3] or [N, 3]
N coordinates to check are within the bounds of the tile
pad : integer or ndarray [3]
anisotropic p... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L477-L499 | [
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valid | Tile.intersection | Intersection of tiles, returned as a tile
>>> Tile.intersection(Tile([0, 1], [5, 4]), Tile([1, 0], [4, 5]))
Tile [1, 1] -> [4, 4] ([3, 3]) | peri/util.py | def intersection(tiles, *args):
"""
Intersection of tiles, returned as a tile
>>> Tile.intersection(Tile([0, 1], [5, 4]), Tile([1, 0], [4, 5]))
Tile [1, 1] -> [4, 4] ([3, 3])
"""
tiles = listify(tiles) + listify(args)
if len(tiles) < 2:
return tiles[... | def intersection(tiles, *args):
"""
Intersection of tiles, returned as a tile
>>> Tile.intersection(Tile([0, 1], [5, 4]), Tile([1, 0], [4, 5]))
Tile [1, 1] -> [4, 4] ([3, 3])
"""
tiles = listify(tiles) + listify(args)
if len(tiles) < 2:
return tiles[... | [
"Intersection",
"of",
"tiles",
"returned",
"as",
"a",
"tile"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L502-L519 | [
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valid | Tile.translate | Translate a tile by an amount dr
>>> Tile(5).translate(1)
Tile [1, 1, 1] -> [6, 6, 6] ([5, 5, 5]) | peri/util.py | def translate(self, dr):
"""
Translate a tile by an amount dr
>>> Tile(5).translate(1)
Tile [1, 1, 1] -> [6, 6, 6] ([5, 5, 5])
"""
tile = self.copy()
tile.l += dr
tile.r += dr
return tile | def translate(self, dr):
"""
Translate a tile by an amount dr
>>> Tile(5).translate(1)
Tile [1, 1, 1] -> [6, 6, 6] ([5, 5, 5])
"""
tile = self.copy()
tile.l += dr
tile.r += dr
return tile | [
"Translate",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L560-L570 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Tile.pad | Pad this tile by an equal amount on each side as specified by pad
>>> Tile(10).pad(2)
Tile [-2, -2, -2] -> [12, 12, 12] ([14, 14, 14])
>>> Tile(10).pad([1,2,3])
Tile [-1, -2, -3] -> [11, 12, 13] ([12, 14, 16]) | peri/util.py | def pad(self, pad):
"""
Pad this tile by an equal amount on each side as specified by pad
>>> Tile(10).pad(2)
Tile [-2, -2, -2] -> [12, 12, 12] ([14, 14, 14])
>>> Tile(10).pad([1,2,3])
Tile [-1, -2, -3] -> [11, 12, 13] ([12, 14, 16])
"""
tile = self.copy... | def pad(self, pad):
"""
Pad this tile by an equal amount on each side as specified by pad
>>> Tile(10).pad(2)
Tile [-2, -2, -2] -> [12, 12, 12] ([14, 14, 14])
>>> Tile(10).pad([1,2,3])
Tile [-1, -2, -3] -> [11, 12, 13] ([12, 14, 16])
"""
tile = self.copy... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L572-L585 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Tile.overhang | Get the left and right absolute overflow -- the amount of box
overhanging `tile`, can be viewed as self \\ tile (set theory relative
complement, but in a bounding sense) | peri/util.py | def overhang(self, tile):
"""
Get the left and right absolute overflow -- the amount of box
overhanging `tile`, can be viewed as self \\ tile (set theory relative
complement, but in a bounding sense)
"""
ll = np.abs(amin(self.l - tile.l, aN(0, dim=self.dim)))
rr =... | def overhang(self, tile):
"""
Get the left and right absolute overflow -- the amount of box
overhanging `tile`, can be viewed as self \\ tile (set theory relative
complement, but in a bounding sense)
"""
ll = np.abs(amin(self.l - tile.l, aN(0, dim=self.dim)))
rr =... | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Tile.reflect_overhang | Compute the overhang and reflect it internally so respect periodic
padding rules (see states._tile_from_particle_change). Returns both
the inner tile and the inner tile with necessary pad. | peri/util.py | def reflect_overhang(self, clip):
"""
Compute the overhang and reflect it internally so respect periodic
padding rules (see states._tile_from_particle_change). Returns both
the inner tile and the inner tile with necessary pad.
"""
orig = self.copy()
tile = self.co... | def reflect_overhang(self, clip):
"""
Compute the overhang and reflect it internally so respect periodic
padding rules (see states._tile_from_particle_change). Returns both
the inner tile and the inner tile with necessary pad.
"""
orig = self.copy()
tile = self.co... | [
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valid | Image.filtered_image | Returns a filtered image after applying the Fourier-space filters | peri/util.py | def filtered_image(self, im):
"""Returns a filtered image after applying the Fourier-space filters"""
q = np.fft.fftn(im)
for k,v in self.filters:
q[k] -= v
return np.real(np.fft.ifftn(q)) | def filtered_image(self, im):
"""Returns a filtered image after applying the Fourier-space filters"""
q = np.fft.fftn(im)
for k,v in self.filters:
q[k] -= v
return np.real(np.fft.ifftn(q)) | [
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"-",
"space",
"filters"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L665-L670 | [
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valid | Image.set_filter | Sets Fourier-space filters for the image. The image is filtered by
subtracting values from the image at slices.
Parameters
----------
slices : List of indices or slice objects.
The q-values in Fourier space to filter.
values : np.ndarray
The complete arra... | peri/util.py | def set_filter(self, slices, values):
"""
Sets Fourier-space filters for the image. The image is filtered by
subtracting values from the image at slices.
Parameters
----------
slices : List of indices or slice objects.
The q-values in Fourier space to filter.... | def set_filter(self, slices, values):
"""
Sets Fourier-space filters for the image. The image is filtered by
subtracting values from the image at slices.
Parameters
----------
slices : List of indices or slice objects.
The q-values in Fourier space to filter.... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L676-L699 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | RawImage.load_image | Read the file and perform any transforms to get a loaded image | peri/util.py | def load_image(self):
""" Read the file and perform any transforms to get a loaded image """
try:
image = initializers.load_tiff(self.filename)
image = initializers.normalize(
image, invert=self.invert, scale=self.exposure,
dtype=self.float_precisi... | def load_image(self):
""" Read the file and perform any transforms to get a loaded image """
try:
image = initializers.load_tiff(self.filename)
image = initializers.normalize(
image, invert=self.invert, scale=self.exposure,
dtype=self.float_precisi... | [
"Read",
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"loaded",
"image"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L793-L805 | [
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valid | RawImage.get_scale | If exposure was not set in the __init__, get the exposure associated
with this RawImage so that it may be used in other
:class:`~peri.util.RawImage`. This is useful for transferring exposure
parameters to a series of images.
Returns
-------
exposure : tuple of floats
... | peri/util.py | def get_scale(self):
"""
If exposure was not set in the __init__, get the exposure associated
with this RawImage so that it may be used in other
:class:`~peri.util.RawImage`. This is useful for transferring exposure
parameters to a series of images.
Returns
-----... | def get_scale(self):
"""
If exposure was not set in the __init__, get the exposure associated
with this RawImage so that it may be used in other
:class:`~peri.util.RawImage`. This is useful for transferring exposure
parameters to a series of images.
Returns
-----... | [
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valid | RawImage.get_scale_from_raw | When given a raw image and the scaled version of the same image, it
extracts the ``exposure`` parameters associated with those images.
This is useful when
Parameters
----------
raw : array_like
The image loaded fresh from a file
scaled : array_like
... | peri/util.py | def get_scale_from_raw(raw, scaled):
"""
When given a raw image and the scaled version of the same image, it
extracts the ``exposure`` parameters associated with those images.
This is useful when
Parameters
----------
raw : array_like
The image loaded... | def get_scale_from_raw(raw, scaled):
"""
When given a raw image and the scaled version of the same image, it
extracts the ``exposure`` parameters associated with those images.
This is useful when
Parameters
----------
raw : array_like
The image loaded... | [
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valid | ProgressBar._draw | Interal draw method, simply prints to screen | peri/util.py | def _draw(self):
""" Interal draw method, simply prints to screen """
if self.display:
print(self._formatstr.format(**self.__dict__), end='')
sys.stdout.flush() | def _draw(self):
""" Interal draw method, simply prints to screen """
if self.display:
print(self._formatstr.format(**self.__dict__), end='')
sys.stdout.flush() | [
"Interal",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L1004-L1008 | [
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valid | ProgressBar.update | Update the value of the progress and update progress bar.
Parameters
-----------
value : integer
The current iteration of the progress | peri/util.py | def update(self, value=0):
"""
Update the value of the progress and update progress bar.
Parameters
-----------
value : integer
The current iteration of the progress
"""
self._deltas.append(time.time())
self.value = value
self._percen... | def update(self, value=0):
"""
Update the value of the progress and update progress bar.
Parameters
-----------
value : integer
The current iteration of the progress
"""
self._deltas.append(time.time())
self.value = value
self._percen... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/util.py#L1013-L1035 | [
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valid | InvenioGroups.init_app | Flask application initialization. | invenio_groups/ext.py | def init_app(self, app):
"""Flask application initialization."""
self.init_config(app)
app.register_blueprint(blueprint)
app.extensions['invenio-groups'] = self | def init_app(self, app):
"""Flask application initialization."""
self.init_config(app)
app.register_blueprint(blueprint)
app.extensions['invenio-groups'] = self | [
"Flask",
"application",
"initialization",
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] | inveniosoftware-contrib/invenio-groups | python | https://github.com/inveniosoftware-contrib/invenio-groups/blob/109481d6b02701db00b72223dd4a65e167c589a6/invenio_groups/ext.py#L40-L44 | [
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valid | Model.check_consistency | Make sure that the required comps are included in the list of
components supplied by the user. Also check that the parameters are
consistent across the many components. | peri/models.py | def check_consistency(self):
"""
Make sure that the required comps are included in the list of
components supplied by the user. Also check that the parameters are
consistent across the many components.
"""
error = False
regex = re.compile('([a-zA-Z_][a-zA-Z0-9_]*)... | def check_consistency(self):
"""
Make sure that the required comps are included in the list of
components supplied by the user. Also check that the parameters are
consistent across the many components.
"""
error = False
regex = re.compile('([a-zA-Z_][a-zA-Z0-9_]*)... | [
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".... | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/models.py#L81-L111 | [
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valid | Model.check_inputs | Check that the list of components `comp` is compatible with both the
varmap and modelstr for this Model | peri/models.py | def check_inputs(self, comps):
"""
Check that the list of components `comp` is compatible with both the
varmap and modelstr for this Model
"""
error = False
compcats = [c.category for c in comps]
# Check that the components are all provided, given the categories
... | def check_inputs(self, comps):
"""
Check that the list of components `comp` is compatible with both the
varmap and modelstr for this Model
"""
error = False
compcats = [c.category for c in comps]
# Check that the components are all provided, given the categories
... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/models.py#L113-L131 | [
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"it... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Model.get_difference_model | Get the equation corresponding to a variation wrt category. For example
if::
modelstr = {
'full' :'H(I) + B',
'dH' : 'dH(I)',
'dI' : 'H(dI)',
'dB' : 'dB'
}
varmap = {'H': 'psf', 'I': 'obj', 'B': 'bkg'}
... | peri/models.py | def get_difference_model(self, category):
"""
Get the equation corresponding to a variation wrt category. For example
if::
modelstr = {
'full' :'H(I) + B',
'dH' : 'dH(I)',
'dI' : 'H(dI)',
'dB' : 'dB'
}
... | def get_difference_model(self, category):
"""
Get the equation corresponding to a variation wrt category. For example
if::
modelstr = {
'full' :'H(I) + B',
'dH' : 'dH(I)',
'dI' : 'H(dI)',
'dB' : 'dB'
}
... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/models.py#L141-L158 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Model.map_vars | Map component function ``funcname`` result into model variables
dictionary for use in eval of the model. If ``diffmap`` is provided then
that symbol is translated into 'd'+diffmap.key and is replaced by
diffmap.value. ``**kwargs` are passed to the ``comp.funcname(**kwargs)``. | peri/models.py | def map_vars(self, comps, funcname='get', diffmap=None, **kwargs):
"""
Map component function ``funcname`` result into model variables
dictionary for use in eval of the model. If ``diffmap`` is provided then
that symbol is translated into 'd'+diffmap.key and is replaced by
diffma... | def map_vars(self, comps, funcname='get', diffmap=None, **kwargs):
"""
Map component function ``funcname`` result into model variables
dictionary for use in eval of the model. If ``diffmap`` is provided then
that symbol is translated into 'd'+diffmap.key and is replaced by
diffma... | [
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... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | Model.evaluate | Calculate the output of a model. It is recommended that at some point
before using `evaluate`, that you make sure the inputs are valid using
:class:`~peri.models.Model.check_inputs`
Parameters
-----------
comps : list of :class:`~peri.comp.comp.Component`
Components ... | peri/models.py | def evaluate(self, comps, funcname='get', diffmap=None, **kwargs):
"""
Calculate the output of a model. It is recommended that at some point
before using `evaluate`, that you make sure the inputs are valid using
:class:`~peri.models.Model.check_inputs`
Parameters
-------... | def evaluate(self, comps, funcname='get', diffmap=None, **kwargs):
"""
Calculate the output of a model. It is recommended that at some point
before using `evaluate`, that you make sure the inputs are valid using
:class:`~peri.models.Model.check_inputs`
Parameters
-------... | [
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valid | lbl | Put a figure label in an axis | peri/viz/plots.py | def lbl(axis, label, size=22):
""" Put a figure label in an axis """
at = AnchoredText(label, loc=2, prop=dict(size=size), frameon=True)
at.patch.set_boxstyle("round,pad=0.,rounding_size=0.0")
#bb = axis.get_yaxis_transform()
#at = AnchoredText(label,
# loc=3, prop=dict(size=18), frameon=... | def lbl(axis, label, size=22):
""" Put a figure label in an axis """
at = AnchoredText(label, loc=2, prop=dict(size=size), frameon=True)
at.patch.set_boxstyle("round,pad=0.,rounding_size=0.0")
#bb = axis.get_yaxis_transform()
#at = AnchoredText(label,
# loc=3, prop=dict(size=18), frameon=... | [
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"label",
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"an",
"axis"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L30-L40 | [
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"p... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | generative_model | Samples x,y,z,r are created by:
b = s.blocks_particle(#)
h = runner.sample_state(s, b, stepout=0.05, N=2000, doprint=True)
z,y,x,r = h.get_histogram().T | peri/viz/plots.py | def generative_model(s,x,y,z,r, factor=1.1):
"""
Samples x,y,z,r are created by:
b = s.blocks_particle(#)
h = runner.sample_state(s, b, stepout=0.05, N=2000, doprint=True)
z,y,x,r = h.get_histogram().T
"""
pl.close('all')
slicez = int(round(z.mean()))
slicex = s.image.shape[2]//2
... | def generative_model(s,x,y,z,r, factor=1.1):
"""
Samples x,y,z,r are created by:
b = s.blocks_particle(#)
h = runner.sample_state(s, b, stepout=0.05, N=2000, doprint=True)
z,y,x,r = h.get_histogram().T
"""
pl.close('all')
slicez = int(round(z.mean()))
slicex = s.image.shape[2]//2
... | [
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valid | examine_unexplained_noise | Compares a state's residuals in real and Fourier space with a Gaussian.
Point out that Fourier space should always be Gaussian and white
Parameters
----------
state : `peri.states.State`
The state to examine.
bins : int or sequence of scalars or str, optional
The nu... | peri/viz/plots.py | def examine_unexplained_noise(state, bins=1000, xlim=(-10,10)):
"""
Compares a state's residuals in real and Fourier space with a Gaussian.
Point out that Fourier space should always be Gaussian and white
Parameters
----------
state : `peri.states.State`
The state to examine.
... | def examine_unexplained_noise(state, bins=1000, xlim=(-10,10)):
"""
Compares a state's residuals in real and Fourier space with a Gaussian.
Point out that Fourier space should always be Gaussian and white
Parameters
----------
state : `peri.states.State`
The state to examine.
... | [
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"#Get the expected ... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | compare_data_model_residuals | Compare the data, model, and residuals of a state.
Makes an image of any 2D slice of a state that compares the data,
model, and residuals. The upper left portion of the image is the raw
data, the central portion the model, and the lower right portion the
image. Either plots the image using plt.imshow()... | peri/viz/plots.py | def compare_data_model_residuals(s, tile, data_vmin='calc', data_vmax='calc',
res_vmin=-0.1, res_vmax=0.1, edgepts='calc', do_imshow=True,
data_cmap=plt.cm.bone, res_cmap=plt.cm.RdBu):
"""
Compare the data, model, and residuals of a state.
Makes an image of any 2D slice of a state that co... | def compare_data_model_residuals(s, tile, data_vmin='calc', data_vmax='calc',
res_vmin=-0.1, res_vmax=0.1, edgepts='calc', do_imshow=True,
data_cmap=plt.cm.bone, res_cmap=plt.cm.RdBu):
"""
Compare the data, model, and residuals of a state.
Makes an image of any 2D slice of a state that co... | [
"Compare",
"the",
"data",
"model",
"and",
"residuals",
"of",
"a",
"state",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L470-L557 | [
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"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | trisect_image | Returns 3 masks that trisect an image into 3 triangular portions.
Parameters
----------
imshape : 2-element list-like of ints
The shape of the image. Elements after the first 2 are ignored.
edgepts : Nested list-like, float, or `calc`, optional.
The vertices of the tria... | peri/viz/plots.py | def trisect_image(imshape, edgepts='calc'):
"""
Returns 3 masks that trisect an image into 3 triangular portions.
Parameters
----------
imshape : 2-element list-like of ints
The shape of the image. Elements after the first 2 are ignored.
edgepts : Nested list-like, float, o... | def trisect_image(imshape, edgepts='calc'):
"""
Returns 3 masks that trisect an image into 3 triangular portions.
Parameters
----------
imshape : 2-element list-like of ints
The shape of the image. Elements after the first 2 are ignored.
edgepts : Nested list-like, float, o... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L559-L610 | [
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"]... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | center_data | Clips data on [vmin, vmax]; then rescales to [0,1] | peri/viz/plots.py | def center_data(data, vmin, vmax):
"""Clips data on [vmin, vmax]; then rescales to [0,1]"""
ans = data - vmin
ans /= (vmax - vmin)
return np.clip(ans, 0, 1) | def center_data(data, vmin, vmax):
"""Clips data on [vmin, vmax]; then rescales to [0,1]"""
ans = data - vmin
ans /= (vmax - vmin)
return np.clip(ans, 0, 1) | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L615-L619 | [
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] | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | sim_crb_diff | each element of std0 should correspond with the element of std1 | peri/viz/plots.py | def sim_crb_diff(std0, std1, N=10000):
""" each element of std0 should correspond with the element of std1 """
a = std0*np.random.randn(N, len(std0))
b = std1*np.random.randn(N, len(std1))
return a - b | def sim_crb_diff(std0, std1, N=10000):
""" each element of std0 should correspond with the element of std1 """
a = std0*np.random.randn(N, len(std0))
b = std1*np.random.randn(N, len(std1))
return a - b | [
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"should",
"correspond",
"with",
"the",
"element",
"of",
"std1"
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L621-L625 | [
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"randn"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | crb_compare | To run, do:
s,h = pickle...
s1,h1 = pickle...
i.e. /media/scratch/bamf/vacancy/vacancy_zoom-1.tif_t002.tif-featured-v2.pkl
i.e. /media/scratch/bamf/frozen-particles/0.tif-featured-full.pkl
crb0 = diag_crb_particles(s); crb1 = diag_crb_particles(s1)
crb_compare(s,h[-25:],s1,h1[-25:], crb... | peri/viz/plots.py | def crb_compare(state0, samples0, state1, samples1, crb0=None, crb1=None,
zlayer=None, xlayer=None):
"""
To run, do:
s,h = pickle...
s1,h1 = pickle...
i.e. /media/scratch/bamf/vacancy/vacancy_zoom-1.tif_t002.tif-featured-v2.pkl
i.e. /media/scratch/bamf/frozen-particles/0.tif-fea... | def crb_compare(state0, samples0, state1, samples1, crb0=None, crb1=None,
zlayer=None, xlayer=None):
"""
To run, do:
s,h = pickle...
s1,h1 = pickle...
i.e. /media/scratch/bamf/vacancy/vacancy_zoom-1.tif_t002.tif-featured-v2.pkl
i.e. /media/scratch/bamf/frozen-particles/0.tif-fea... | [
"To",
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/viz/plots.py#L643-L864 | [
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"h... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | twoslice | Plot two parts of the ortho view, the two sections given by ``orientation``. | peri/viz/plots.py | def twoslice(field, center=None, size=6.0, cmap='bone_r', vmin=0, vmax=1,
orientation='vertical', figpad=1.09, off=0.01):
"""
Plot two parts of the ortho view, the two sections given by ``orientation``.
"""
center = center or [i//2 for i in field.shape]
slices = []
for i,c in enumerate(c... | def twoslice(field, center=None, size=6.0, cmap='bone_r', vmin=0, vmax=1,
orientation='vertical', figpad=1.09, off=0.01):
"""
Plot two parts of the ortho view, the two sections given by ``orientation``.
"""
center = center or [i//2 for i in field.shape]
slices = []
for i,c in enumerate(c... | [
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valid | circles | Plots a set of circles corresponding to a slice through the platonic
structure. Copied from twoslice_overlay with comments, standaloneness.
Inputs
------
pos : array of particle positions; [N,3]
rad : array of particle radii; [N]
ax : plt.axis instance
layer : Which layer of... | peri/viz/plots.py | def circles(st, layer, axis, ax=None, talpha=1.0, cedge='white', cface='white'):
"""
Plots a set of circles corresponding to a slice through the platonic
structure. Copied from twoslice_overlay with comments, standaloneness.
Inputs
------
pos : array of particle positions; [N,3]
rad... | def circles(st, layer, axis, ax=None, talpha=1.0, cedge='white', cface='white'):
"""
Plots a set of circles corresponding to a slice through the platonic
structure. Copied from twoslice_overlay with comments, standaloneness.
Inputs
------
pos : array of particle positions; [N,3]
rad... | [
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valid | missing_particle | create a two particle state and compare it to featuring using a single particle guess | scripts/does_matter/missing-particle.py | def missing_particle(separation=0.0, radius=RADIUS, SNR=20):
""" create a two particle state and compare it to featuring using a single particle guess """
# create a base image of one particle
s = init.create_two_particle_state(imsize=6*radius+4, axis='x', sigma=1.0/SNR,
delta=separation, radius... | def missing_particle(separation=0.0, radius=RADIUS, SNR=20):
""" create a two particle state and compare it to featuring using a single particle guess """
# create a base image of one particle
s = init.create_two_particle_state(imsize=6*radius+4, axis='x', sigma=1.0/SNR,
delta=separation, radius... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/scripts/does_matter/missing-particle.py#L11-L19 | [
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"radius",
"+",
... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_rand_Japprox | Calculates a random approximation to J by returning J only at a
set of random pixel/voxel locations.
Parameters
----------
s : :class:`peri.states.State`
The state to calculate J for.
params : List
The list of parameter names to calculate the gradient of.
num... | peri/opt/optimize.py | def get_rand_Japprox(s, params, num_inds=1000, include_cost=False, **kwargs):
"""
Calculates a random approximation to J by returning J only at a
set of random pixel/voxel locations.
Parameters
----------
s : :class:`peri.states.State`
The state to calculate J for.
param... | def get_rand_Japprox(s, params, num_inds=1000, include_cost=False, **kwargs):
"""
Calculates a random approximation to J by returning J only at a
set of random pixel/voxel locations.
Parameters
----------
s : :class:`peri.states.State`
The state to calculate J for.
param... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/opt/optimize.py#L64-L114 | [
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"siz... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | name_globals | Returns a list of the global parameter names.
Parameters
----------
s : :class:`peri.states.ImageState`
The state to name the globals of.
remove_params : Set or None
A set of unique additional parameters to remove from the globals
list.
Returns
-----... | peri/opt/optimize.py | def name_globals(s, remove_params=None):
"""
Returns a list of the global parameter names.
Parameters
----------
s : :class:`peri.states.ImageState`
The state to name the globals of.
remove_params : Set or None
A set of unique additional parameters to remove from... | def name_globals(s, remove_params=None):
"""
Returns a list of the global parameter names.
Parameters
----------
s : :class:`peri.states.ImageState`
The state to name the globals of.
remove_params : Set or None
A set of unique additional parameters to remove from... | [
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"names",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/opt/optimize.py#L116-L140 | [
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"... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | get_num_px_jtj | Calculates the number of pixels to use for J at a given memory usage.
Tries to pick a number of pixels as (size of image / `decimate`).
However, clips this to a maximum size and minimum size to ensure that
(1) too much memory isn't used and (2) J has enough elements so that
the inverse of JTJ will be w... | peri/opt/optimize.py | def get_num_px_jtj(s, nparams, decimate=1, max_mem=1e9, min_redundant=20):
"""
Calculates the number of pixels to use for J at a given memory usage.
Tries to pick a number of pixels as (size of image / `decimate`).
However, clips this to a maximum size and minimum size to ensure that
(1) too much m... | def get_num_px_jtj(s, nparams, decimate=1, max_mem=1e9, min_redundant=20):
"""
Calculates the number of pixels to use for J at a given memory usage.
Tries to pick a number of pixels as (size of image / `decimate`).
However, clips this to a maximum size and minimum size to ensure that
(1) too much m... | [
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"to",
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"for",
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"usage",
"."
] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/opt/optimize.py#L142-L183 | [
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"#... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
valid | vectorize_damping | Returns a non-constant damping vector, allowing certain parameters to be
more strongly damped than others.
Parameters
----------
params : List
The list of parameter names, in order.
damping : Float
The default value of the damping.
increase_list: List
... | peri/opt/optimize.py | def vectorize_damping(params, damping=1.0, increase_list=[['psf-', 1e4]]):
"""
Returns a non-constant damping vector, allowing certain parameters to be
more strongly damped than others.
Parameters
----------
params : List
The list of parameter names, in order.
damping : ... | def vectorize_damping(params, damping=1.0, increase_list=[['psf-', 1e4]]):
"""
Returns a non-constant damping vector, allowing certain parameters to be
more strongly damped than others.
Parameters
----------
params : List
The list of parameter names, in order.
damping : ... | [
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] | peri-source/peri | python | https://github.com/peri-source/peri/blob/61beed5deaaf978ab31ed716e8470d86ba639867/peri/opt/optimize.py#L185-L210 | [
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"n... | 61beed5deaaf978ab31ed716e8470d86ba639867 |
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