INSTRUCTION
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Draw edges as Bézier curves.
|
def connect(self, axis0, n0_index, source_angle, axis1, n1_index, target_angle, **kwargs):
"""Draw edges as Bézier curves.
Start and end points map to the coordinates of the given nodes
which in turn are set when adding nodes to an axis with the
Axis.add_node() method, by using the placement information of
the axis and a specified offset from its start point.
Control points are set at the same distance from the start (or end)
point of an axis as their corresponding nodes, but along an invisible
axis that shares its origin but diverges by a given angle.
Parameters
----------
axis0 : source Axis object
n0_index : key of source node in nodes dictionary of axis0
source_angle : angle of departure for invisible axis that diverges from axis0 and holds first control points
axis1 : target Axis object
n1_index : key of target node in nodes dictionary of axis1
target_angle : angle of departure for invisible axis that diverges from axis1 and holds second control points
kwargs : extra SVG attributes for path element, optional
Set or change attributes using key=value
"""
n0 = axis0.nodes[n0_index]
n1 = axis1.nodes[n1_index]
pth = self.dwg.path(d="M %s %s" % (n0.x, n0.y), fill='none', **kwargs) # source
# compute source control point
alfa = axis0.angle() + radians(source_angle)
length = sqrt( ((n0.x - axis0.start[0])**2) + ((n0.y-axis0.start[1])**2))
x = axis0.start[0] + length * cos(alfa);
y = axis0.start[1] + length * sin(alfa);
pth.push("C %s %s" % (x, y)) # first control point in path
# compute target control point
alfa = axis1.angle() + radians(target_angle)
length = sqrt( ((n1.x - axis1.start[0])**2) + ((n1.y-axis1.start[1])**2))
x = axis1.start[0] + length * cos(alfa);
y = axis1.start[1] + length * sin(alfa);
pth.push("%s %s" % (x, y)) # second control point in path
pth.push("%s %s" % (n1.x, n1.y)) # target
self.dwg.add(pth)
|
Add a Node object to nodes dictionary calculating its coordinates using offset
|
def add_node(self, node, offset):
"""Add a Node object to nodes dictionary, calculating its coordinates using offset
Parameters
----------
node : a Node object
offset : float
number between 0 and 1 that sets the distance
from the start point at which the node will be placed
"""
# calculate x,y from offset considering axis start and end points
width = self.end[0] - self.start[0]
height = self.end[1] - self.start[1]
node.x = self.start[0] + (width * offset)
node.y = self.start[1] + (height * offset)
self.nodes[node.ID] = node
|
Hunt down the settings. py module by going up the FS path
|
def get_settings_path(settings_module):
'''
Hunt down the settings.py module by going up the FS path
'''
cwd = os.getcwd()
settings_filename = '%s.py' % (
settings_module.split('.')[-1]
)
while cwd:
if settings_filename in os.listdir(cwd):
break
cwd = os.path.split(cwd)[0]
if os.name == 'nt' and NT_ROOT.match(cwd):
return None
elif cwd == '/':
return None
return cwd
|
Create the test database and schema if needed and switch the connection over to that database. Then call install () to install all apps listed in the loaded settings module.
|
def begin(self):
"""
Create the test database and schema, if needed, and switch the
connection over to that database. Then call install() to install
all apps listed in the loaded settings module.
"""
for plugin in self.nose_config.plugins.plugins:
if getattr(plugin, 'django_plugin', False):
self.django_plugins.append(plugin)
os.environ['DJANGO_SETTINGS_MODULE'] = self.settings_module
if self.conf.addPaths:
map(add_path, self.conf.where)
try:
__import__(self.settings_module)
self.settings_path = self.settings_module
except ImportError:
# Settings module is not found in PYTHONPATH. Try to do
# some funky backwards crawling in directory tree, ie. add
# the working directory (and any package parents) to
# sys.path before trying to import django modules;
# otherwise, they won't be able to find project.settings
# if the working dir is project/ or project/..
self.settings_path = get_settings_path(self.settings_module)
if not self.settings_path:
# short circuit if no settings file can be found
raise RuntimeError("Can't find Django settings file!")
add_path(self.settings_path)
sys.path.append(self.settings_path)
from django.conf import settings
# Some Django code paths evaluate differently
# between DEBUG and not DEBUG. Example of this include the url
# dispatcher when 404's are hit. Django's own test runner forces DEBUG
# to be off.
settings.DEBUG = False
self.call_plugins_method('beforeConnectionSetup', settings)
from django.core import management
from django.test.utils import setup_test_environment
if hasattr(settings, 'DATABASES'):
self.old_db = settings.DATABASES['default']['NAME']
else:
self.old_db = settings.DATABASE_NAME
from django.db import connections
self._monkeypatch_test_classes()
for connection in connections.all():
self.call_plugins_method(
'beforeTestSetup', settings, setup_test_environment,
connection)
try:
setup_test_environment()
except RuntimeError: # Django 1.11 + multiprocess this happens.
pass
import django
if hasattr(django, 'setup'):
django.setup()
self.call_plugins_method('afterTestSetup', settings)
management.get_commands()
# Ensure that nothing (eg. South) steals away our syncdb command
if self.django_version < self.DJANGO_1_7:
management._commands['syncdb'] = 'django.core'
for connection in connections.all():
self.call_plugins_method(
'beforeTestDb', settings, connection, management)
connection.creation.create_test_db(
verbosity=self.verbosity,
autoclobber=True,
)
logger.debug("Running syncdb")
self._num_syncdb_calls += 1
self.call_plugins_method('afterTestDb', settings, connection)
self.store_original_transaction_methods()
|
Determine if the given test supports transaction management for database rollback test isolation and also whether or not the test has opted out of that support.
|
def _should_use_transaction_isolation(self, test, settings):
"""
Determine if the given test supports transaction management for
database rollback test isolation and also whether or not the test has
opted out of that support.
Transactions make database rollback much quicker when supported, with
the caveat that any tests that are explicitly testing transactions
won't work properly and any tests that depend on external access to the
test database won't be able to view data created/altered during the
test.
"""
if not getattr(test.context, 'use_transaction_isolation', True):
# The test explicitly says not to use transaction isolation
return False
if getattr(settings, 'DISABLE_TRANSACTION_MANAGEMENT', False):
# Do not use transactions if user has forbidden usage.
return False
if hasattr(settings, 'DATABASE_SUPPORTS_TRANSACTIONS'):
if not settings.DATABASE_SUPPORTS_TRANSACTIONS:
# The DB doesn't support transactions. Don't try it
return False
return True
|
Clean up any created database and schema.
|
def finalize(self, result=None):
"""
Clean up any created database and schema.
"""
if not self.settings_path:
# short circuit if no settings file can be found
return
from django.test.utils import teardown_test_environment
from django.db import connection
from django.conf import settings
self.call_plugins_method('beforeDestroyTestDb', settings, connection)
try:
connection.creation.destroy_test_db(
self.old_db,
verbosity=self.verbosity,
)
except Exception:
# If we can't tear down the test DB, don't worry about it.
pass
self.call_plugins_method('afterDestroyTestDb', settings, connection)
self.call_plugins_method(
'beforeTeardownTestEnv', settings, teardown_test_environment)
teardown_test_environment()
self.call_plugins_method('afterTeardownTestEnv', settings)
|
Truncates field to 0 1 ; then normalizes to a uin8 on [ 0 255 ]
|
def norm(field, vmin=0, vmax=255):
"""Truncates field to 0,1; then normalizes to a uin8 on [0,255]"""
field = 255*np.clip(field, 0, 1)
field = field.astype('uint8')
return field
|
Given a state extracts a field. Extracted value depends on the value of field: exp - particles: The inverted data in the regions of the particles zeros otherwise -- i. e. particles + noise. exp - platonic: Same as above but nonzero in the region of the entire platonic image -- i. e. platonic + noise. sim - particles: Just the particles image ; no noise from the data. sim - platonic: Just the platonic image ; no noise from the data.
|
def extract_field(state, field='exp-particles'):
"""
Given a state, extracts a field. Extracted value depends on the value
of field:
'exp-particles' : The inverted data in the regions of the particles,
zeros otherwise -- i.e. particles + noise.
'exp-platonic' : Same as above, but nonzero in the region of the
entire platonic image -- i.e. platonic + noise.
'sim-particles' : Just the particles image; no noise from the data.
'sim-platonic' : Just the platonic image; no noise from the data.
"""
es, pp = field.split('-') #exp vs sim, particles vs platonic
#1. The weights for the field, based off the platonic vs particles
if pp == 'particles':
o = state.get('obj')
if isinstance(o, peri.comp.comp.ComponentCollection):
wts = 0*o.get()[state.inner]
for c in o.comps:
if isinstance(c, peri.comp.objs.PlatonicSpheresCollection):
wts += c.get()[state.inner]
else:
wts = o.get()[state.inner]
elif pp == 'platonic':
wts = state.get('obj').get()[state.inner]
else:
raise ValueError('Not a proper field.')
#2. Exp vs sim-like data
if es == 'exp':
out = (1-state.data) * (wts > 1e-5)
elif es == 'sim':
out = wts
else:
raise ValueError('Not a proper field.')
return norm(clip(roll(out)))
|
Uses vtk to make render an image of a field with control over the camera angle and colormap.
|
def volume_render(field, outfile, maxopacity=1.0, cmap='bone',
size=600, elevation=45, azimuth=45, bkg=(0.0, 0.0, 0.0),
opacitycut=0.35, offscreen=False, rayfunction='smart'):
"""
Uses vtk to make render an image of a field, with control over the
camera angle and colormap.
Input Parameters
----------------
field : np.ndarray
3D array of the field to render.
outfile : string
The save name of the image.
maxopacity : Float
Default is 1.0
cmap : matplotlib colormap string
Passed to cmap2colorfunc. Default is bone.
size : 2-element list-like of ints or Int
The size of the final rendered image.
elevation : Numeric
The elevation of the camera angle, in degrees. Default is 45
azimuth : Numeric
The azimuth of the camera angle, in degrees. Default is 45
bkg : Tuple of floats
3-element tuple of floats on [0,1] of the background image color.
Default is (0., 0., 0.).
"""
sh = field.shape
dataImporter = vtk.vtkImageImport()
dataImporter.SetDataScalarTypeToUnsignedChar()
data_string = field.tostring()
dataImporter.SetNumberOfScalarComponents(1)
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
dataImporter.SetDataExtent(0, sh[2]-1, 0, sh[1]-1, 0, sh[0]-1)
dataImporter.SetWholeExtent(0, sh[2]-1, 0, sh[1]-1, 0, sh[0]-1)
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
alphaChannelFunc.AddPoint(int(255*opacitycut), maxopacity)
volumeProperty = vtk.vtkVolumeProperty()
colorFunc = cmap2colorfunc(cmap)
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeMapper = vtk.vtkVolumeRayCastMapper()
if rayfunction == 'mip':
comp = vtk.vtkVolumeRayCastMIPFunction()
comp.SetMaximizeMethodToOpacity()
elif rayfunction == 'avg':
comp = vtk.vtkVolumeRayCastCompositeFunction()
elif rayfunction == 'iso':
comp = vtk.vtkVolumeRayCastIsosurfaceFunction()
comp.SetIsoValue(maxopacity/2)
else:
comp = vtk.vtkVolumeRayCastIsosurfaceFunction()
volumeMapper.SetSampleDistance(0.1)
volumeMapper.SetVolumeRayCastFunction(comp)
if rayfunction == 'smart':
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
light = vtk.vtkLight()
light.SetLightType(vtk.VTK_LIGHT_TYPE_HEADLIGHT)
light.SetIntensity(5.5)
light.SwitchOn()
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderWin.SetOffScreenRendering(1);
if not hasattr(size, '__iter__'):
size = (size, size)
renderer.AddVolume(volume)
renderer.AddLight(light)
renderer.SetBackground(*bkg)
renderWin.SetSize(*size)
if offscreen:
renderWin.SetOffScreenRendering(1)
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
renderWin.AddObserver("AbortCheckEvent", exitCheck)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.Initialize()
renderWin.Render()
renderInteractor.Start()
#writer = vtk.vtkFFMPEGWriter()
#writer.SetQuality(2)
#writer.SetRate(24)
#w2i = vtk.vtkWindowToImageFilter()
#w2i.SetInput(renderWin)
#writer.SetInputConnection(w2i.GetOutputPort())
#writer.SetFileName('movie.avi')
#writer.Start()
#writer.End()
writer = vtk.vtkPNGWriter()
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(renderWin)
writer.SetInputConnection(w2i.GetOutputPort())
renderWin.Render()
ac = renderer.GetActiveCamera()
ac.Elevation(elevation)
ac.Azimuth(azimuth)
renderer.ResetCameraClippingRange()
renderWin.Render()
w2i.Modified()
writer.SetFileName(outfile)
writer.Write()
|
Makes a matplotlib. pyplot. Figure without tooltips or keybindings
|
def make_clean_figure(figsize, remove_tooltips=False, remove_keybindings=False):
"""
Makes a `matplotlib.pyplot.Figure` without tooltips or keybindings
Parameters
----------
figsize : tuple
Figsize as passed to `matplotlib.pyplot.figure`
remove_tooltips, remove_keybindings : bool
Set to True to remove the tooltips bar or any key bindings,
respectively. Default is False
Returns
-------
fig : `matplotlib.pyplot.Figure`
"""
tooltip = mpl.rcParams['toolbar']
if remove_tooltips:
mpl.rcParams['toolbar'] = 'None'
fig = pl.figure(figsize=figsize)
mpl.rcParams['toolbar'] = tooltip
if remove_keybindings:
fig.canvas.mpl_disconnect(fig.canvas.manager.key_press_handler_id)
return fig
|
Draws a gaussian range is ( 0 1 ]. Coords = [ 3 n ]
|
def _particle_func(self, coords, pos, wid):
"""Draws a gaussian, range is (0,1]. Coords = [3,n]"""
dx, dy, dz = [c - p for c,p in zip(coords, pos)]
dr2 = dx*dx + dy*dy + dz*dz
return np.exp(-dr2/(2*wid*wid))
|
updates self. field
|
def update_field(self, poses=None):
"""updates self.field"""
m = np.clip(self.particle_field, 0, 1)
part_color = np.zeros(self._image.shape)
for a in range(4): part_color[:,:,:,a] = self.part_col[a]
self.field = np.zeros(self._image.shape)
for a in range(4):
self.field[:,:,:,a] = m*part_color[:,:,:,a] + (1-m) * self._image[:,:,:,a]
|
removes the closest particle in self. pos to p
|
def _remove_closest_particle(self, p):
"""removes the closest particle in self.pos to ``p``"""
#1. find closest pos:
dp = self.pos - p
dist2 = (dp*dp).sum(axis=1)
ind = dist2.argmin()
rp = self.pos[ind].copy()
#2. delete
self.pos = np.delete(self.pos, ind, axis=0)
return rp
|
See diffusion_correlated for information related to units etc
|
def diffusion(diffusion_constant=0.2, exposure_time=0.05, samples=200):
"""
See `diffusion_correlated` for information related to units, etc
"""
radius = 5
psfsize = np.array([2.0, 1.0, 3.0])
# create a base image of one particle
s0 = init.create_single_particle_state(imsize=4*radius,
radius=radius, psfargs={'params': psfsize, 'error': 1e-6})
# add up a bunch of trajectories
finalimage = 0*s0.get_model_image()[s0.inner]
position = 0*s0.obj.pos[0]
for i in xrange(samples):
offset = np.sqrt(6*diffusion_constant*exposure_time)*np.random.randn(3)
s0.obj.pos[0] = np.array(s0.image.shape)/2 + offset
s0.reset()
finalimage += s0.get_model_image()[s0.inner]
position += s0.obj.pos[0]
finalimage /= float(samples)
position /= float(samples)
# place that into a new image at the expected parameters
s = init.create_single_particle_state(imsize=4*radius, sigma=0.05,
radius=radius, psfargs={'params': psfsize, 'error': 1e-6})
s.reset()
# measure the true inferred parameters
return s, finalimage, position
|
Calculate the ( perhaps ) correlated diffusion effect between particles during the exposure time of the confocal microscope. diffusion_constant is in terms of seconds and pixel sizes exposure_time is in seconds
|
def diffusion_correlated(diffusion_constant=0.2, exposure_time=0.05,
samples=40, phi=0.25):
"""
Calculate the (perhaps) correlated diffusion effect between particles
during the exposure time of the confocal microscope. diffusion_constant is
in terms of seconds and pixel sizes exposure_time is in seconds
1 micron radius particle:
D = kT / (6 a\pi\eta)
for 80/20 g/w (60 mPas), 3600 nm^2/sec ~ 0.15 px^2/sec
for 100 % w (0.9 mPas), ~ 10.1 px^2/sec
a full 60 layer scan takes 0.1 sec, so a particle is 0.016 sec exposure
"""
radius = 5
psfsize = np.array([2.0, 1.0, 3.0])/2
pos, rad, tile = nbody.initialize_particles(N=50, phi=phi, polydispersity=0.0)
sim = nbody.BrownianHardSphereSimulation(
pos, rad, tile, D=diffusion_constant, dt=exposure_time/samples
)
sim.dt = 1e-2
sim.relax(2000)
sim.dt = exposure_time/samples
# move the center to index 0 for easier analysis later
c = ((sim.pos - sim.tile.center())**2).sum(axis=-1).argmin()
pc = sim.pos[c].copy()
sim.pos[c] = sim.pos[0]
sim.pos[0] = pc
# which particles do we want to simulate motion for? particle
# zero and its neighbors
mask = np.zeros_like(sim.rad).astype('bool')
neigh = sim.neighbors(3*radius, 0)
for i in neigh+[0]:
mask[i] = True
img = np.zeros(sim.tile.shape)
s0 = runner.create_state(img, sim.pos, sim.rad, ignoreimage=True)
# add up a bunch of trajectories
finalimage = 0*s0.get_model_image()[s0.inner]
position = 0*s0.obj.pos
for i in xrange(samples):
sim.step(1, mask=mask)
s0.obj.pos = sim.pos.copy() + s0.pad
s0.reset()
finalimage += s0.get_model_image()[s0.inner]
position += s0.obj.pos
finalimage /= float(samples)
position /= float(samples)
# place that into a new image at the expected parameters
s = runner.create_state(img, sim.pos, sim.rad, ignoreimage=True)
s.reset()
# measure the true inferred parameters
return s, finalimage, position
|
we want to display the errors introduced by pixelation so we plot: * CRB sampled error vs exposure time
|
def dorun(SNR=20, ntimes=20, samples=10, noise_samples=10, sweeps=20, burn=10,
correlated=False):
"""
we want to display the errors introduced by pixelation so we plot:
* CRB, sampled error vs exposure time
a = dorun(ntimes=10, samples=5, noise_samples=5, sweeps=20, burn=8)
"""
if not correlated:
times = np.logspace(-3, 0, ntimes)
else:
times = np.logspace(np.log10(0.05), np.log10(30), ntimes)
crbs, vals, errs, poss = [], [], [], []
for i,t in enumerate(times):
print '###### time', i, t
for j in xrange(samples):
print 'image', j, '|',
if not correlated:
s,im,pos = diffusion(diffusion_constant=0.2, exposure_time=t)
else:
s,im,pos = diffusion_correlated(diffusion_constant=0.2, exposure_time=t)
# typical image
common.set_image(s, im, 1.0/SNR)
crbs.append(common.crb(s))
val, err = common.sample(s, im, 1.0/SNR, N=noise_samples, sweeps=sweeps, burn=burn)
poss.append(pos)
vals.append(val)
errs.append(err)
shape0 = (ntimes, samples, -1)
shape1 = (ntimes, samples, noise_samples, -1)
crbs = np.array(crbs).reshape(shape0)
vals = np.array(vals).reshape(shape1)
errs = np.array(errs).reshape(shape1)
poss = np.array(poss).reshape(shape0)
return [crbs, vals, errs, poss, times]
|
Makes a guess at particle positions using heuristic centroid methods.
|
def feature_guess(st, rad, invert='guess', minmass=None, use_tp=False,
trim_edge=False, **kwargs):
"""
Makes a guess at particle positions using heuristic centroid methods.
Parameters
----------
st : :class:`peri.states.State`
The state to check adding particles to.
rad : Float
The feature size for featuring.
invert : {'guess', True, False}, optional
Whether to invert the image; set to True for there are dark
particles on a bright background, False for bright particles.
The default is to guess from the state's current particles.
minmass : Float or None, optional
The minimum mass/masscut of a particle. Default is ``None`` =
calculated internally.
use_tp : Bool, optional
Whether or not to use trackpy. Default is ``False``, since trackpy
cuts out particles at the edge.
trim_edge : Bool, optional
Whether to trim particles at the edge pixels of the image. Can be
useful for initial featuring but is bad for adding missing particles
as they are frequently at the edge. Default is ``False``.
Returns
-------
guess : [N,3] numpy.ndarray
The featured positions of the particles, sorted in order of decreasing
feature mass.
npart : Int
The number of added particles.
"""
# FIXME does not use the **kwargs, but needs b/c called with wrong kwargs
if invert == 'guess':
invert = guess_invert(st)
if invert:
im = 1 - st.residuals
else:
im = st.residuals
return _feature_guess(im, rad, minmass=minmass, use_tp=use_tp,
trim_edge=trim_edge)
|
Workhorse of feature_guess
|
def _feature_guess(im, rad, minmass=None, use_tp=False, trim_edge=False):
"""Workhorse of feature_guess"""
if minmass is None:
# we use 1% of the feature size mass as a cutoff;
# it's easier to remove than to add
minmass = rad**3 * 4/3.*np.pi * 0.01
# 0.03 is a magic number; works well
if use_tp:
diameter = np.ceil(2*rad)
diameter += 1-(diameter % 2)
df = peri.trackpy.locate(im, int(diameter), minmass=minmass)
npart = np.array(df['mass']).size
guess = np.zeros([npart, 3])
guess[:, 0] = df['z']
guess[:, 1] = df['y']
guess[:, 2] = df['x']
mass = df['mass']
else:
guess, mass = initializers.local_max_featuring(
im, radius=rad, minmass=minmass, trim_edge=trim_edge)
npart = guess.shape[0]
# I want to return these sorted by mass:
inds = np.argsort(mass)[::-1] # biggest mass first
return guess[inds].copy(), npart
|
Checks whether to add particles at a given position by seeing if adding the particle improves the fit of the state.
|
def check_add_particles(st, guess, rad='calc', do_opt=True, im_change_frac=0.2,
min_derr='3sig', **kwargs):
"""
Checks whether to add particles at a given position by seeing if adding
the particle improves the fit of the state.
Parameters
----------
st : :class:`peri.states.State`
The state to check adding particles to.
guess : [N,3] list-like
The positions of particles to check to add.
rad : {Float, ``'calc'``}, optional.
The radius of the newly-added particles. Default is ``'calc'``,
which uses the states current radii's median.
do_opt : Bool, optional
Whether to optimize the particle position before checking if it
should be kept. Default is True (optimizes position).
im_change_frac : Float
How good the change in error needs to be relative to the change in
the difference image. Default is 0.2; i.e. if the error does not
decrease by 20% of the change in the difference image, do not add
the particle.
min_derr : Float or '3sig'
The minimal improvement in error to add a particle. Default
is ``'3sig' = 3*st.sigma``.
Returns
-------
accepts : Int
The number of added particles
new_poses : [N,3] list
List of the positions of the added particles. If ``do_opt==True``,
then these positions will differ from the input 'guess'.
"""
# FIXME does not use the **kwargs, but needs b/c called with wrong kwargs
if min_derr == '3sig':
min_derr = 3 * st.sigma
accepts = 0
new_poses = []
if rad == 'calc':
rad = guess_add_radii(st)
message = ('-'*30 + 'ADDING' + '-'*30 +
'\n Z\t Y\t X\t R\t|\t ERR0\t\t ERR1')
with log.noformat():
CLOG.info(message)
for a in range(guess.shape[0]):
p0 = guess[a]
absent_err = st.error
absent_d = st.residuals.copy()
ind = st.obj_add_particle(p0, rad)
if do_opt:
# the slowest part of this
opt.do_levmarq_particles(
st, ind, damping=1.0, max_iter=1, run_length=3,
eig_update=False, include_rad=False)
present_err = st.error
present_d = st.residuals.copy()
dont_kill = should_particle_exist(
absent_err, present_err, absent_d, present_d,
im_change_frac=im_change_frac, min_derr=min_derr)
if dont_kill:
accepts += 1
p = tuple(st.obj_get_positions()[ind].ravel())
r = tuple(st.obj_get_radii()[ind].ravel())
new_poses.append(p)
part_msg = '%2.2f\t%3.2f\t%3.2f\t%3.2f\t|\t%4.3f \t%4.3f' % (
p + r + (absent_err, st.error))
with log.noformat():
CLOG.info(part_msg)
else:
st.obj_remove_particle(ind)
if np.abs(absent_err - st.error) > 1e-4:
raise RuntimeError('updates not exact?')
return accepts, new_poses
|
Checks whether to remove particle ind from state st. If removing the particle increases the error by less than max ( min_derr change in image * im_change_frac ) then the particle is removed.
|
def check_remove_particle(st, ind, im_change_frac=0.2, min_derr='3sig',
**kwargs):
"""
Checks whether to remove particle 'ind' from state 'st'. If removing the
particle increases the error by less than max( min_derr, change in image *
im_change_frac), then the particle is removed.
Parameters
----------
st : :class:`peri.states.State`
The state to check adding particles to.
ind : Int
The index of the particle to check to remove.
im_change_frac : Float
How good the change in error needs to be relative to the change in
the difference image. Default is 0.2; i.e. if the error does not
decrease by 20% of the change in the difference image, do not add
the particle.
min_derr : Float or '3sig'
The minimal improvement in error to add a particle. Default is
``'3sig' = 3*st.sigma``.
Returns
-------
killed : Bool
Whether the particle was removed.
p : Tuple
The position of the removed particle.
r : Tuple
The radius of the removed particle.
"""
# FIXME does not use the **kwargs, but needs b/c called with wrong kwargs
if min_derr == '3sig':
min_derr = 3 * st.sigma
present_err = st.error
present_d = st.residuals.copy()
p, r = st.obj_remove_particle(ind)
p = p[0]
r = r[0]
absent_err = st.error
absent_d = st.residuals.copy()
if should_particle_exist(absent_err, present_err, absent_d, present_d,
im_change_frac=im_change_frac, min_derr=min_derr):
st.obj_add_particle(p, r)
killed = False
else:
killed = True
return killed, tuple(p), (r,)
|
Checks whether or not adding a particle should be present.
|
def should_particle_exist(absent_err, present_err, absent_d, present_d,
im_change_frac=0.2, min_derr=0.1):
"""
Checks whether or not adding a particle should be present.
Parameters
----------
absent_err : Float
The state error without the particle.
present_err : Float
The state error with the particle.
absent_d : numpy.ndarray
The state residuals without the particle.
present_d : numpy.ndarray
The state residuals with the particle.
im_change_frac : Float, optional
How good the change in error needs to be relative to the change in
the residuals. Default is 0.2; i.e. return False if the error does
not decrease by 0.2 x the change in the residuals.
min_derr : Float, optional
The minimal improvement in error. Default is 0.1
Returns
-------
Bool
True if the errors is better with the particle present.
"""
delta_im = np.ravel(present_d - absent_d)
im_change = np.dot(delta_im, delta_im)
err_cutoff = max([im_change_frac * im_change, min_derr])
return (absent_err - present_err) >= err_cutoff
|
Attempts to add missing particles to the state.
|
def add_missing_particles(st, rad='calc', tries=50, **kwargs):
"""
Attempts to add missing particles to the state.
Operates by:
(1) featuring the difference image using feature_guess,
(2) attempting to add the featured positions using check_add_particles.
Parameters
----------
st : :class:`peri.states.State`
The state to check adding particles to.
rad : Float or 'calc', optional
The radius of the newly-added particles and of the feature size for
featuring. Default is 'calc', which uses the median of the state's
current radii.
tries : Int, optional
How many particles to attempt to add. Only tries to add the first
``tries`` particles, in order of mass. Default is 50.
Other Parameters
----------------
invert : Bool, optional
Whether to invert the image. Default is ``True``, i.e. dark particles
minmass : Float or None, optionals
The minimum mass/masscut of a particle. Default is ``None``=calcualted
by ``feature_guess``.
use_tp : Bool, optional
Whether to use trackpy in feature_guess. Default is False, since
trackpy cuts out particles at the edge.
do_opt : Bool, optional
Whether to optimize the particle position before checking if it
should be kept. Default is True (optimizes position).
im_change_frac : Float, optional
How good the change in error needs to be relative to the change
in the difference image. Default is 0.2; i.e. if the error does
not decrease by 20% of the change in the difference image, do
not add the particle.
min_derr : Float or '3sig', optional
The minimal improvement in error to add a particle. Default
is ``'3sig' = 3*st.sigma``.
Returns
-------
accepts : Int
The number of added particles
new_poses : [N,3] list
List of the positions of the added particles. If ``do_opt==True``,
then these positions will differ from the input 'guess'.
"""
if rad == 'calc':
rad = guess_add_radii(st)
guess, npart = feature_guess(st, rad, **kwargs)
tries = np.min([tries, npart])
accepts, new_poses = check_add_particles(
st, guess[:tries], rad=rad, **kwargs)
return accepts, new_poses
|
Removes improperly - featured particles from the state based on a combination of particle size and the change in error on removal.
|
def remove_bad_particles(st, min_rad='calc', max_rad='calc', min_edge_dist=2.0,
check_rad_cutoff=[3.5, 15], check_outside_im=True,
tries=50, im_change_frac=0.2, **kwargs):
"""
Removes improperly-featured particles from the state, based on a
combination of particle size and the change in error on removal.
Parameters
-----------
st : :class:`peri.states.State`
The state to remove bad particles from.
min_rad : Float, optional
All particles with radius below min_rad are automatically deleted.
Set to 'calc' to make it the median rad - 25* radius std.
Default is 'calc'.
max_rad : Float, optional
All particles with radius above max_rad are automatically deleted.
Set to 'calc' to make it the median rad + 15* radius std.
Default is 'calc'.
min_edge_dist : Float, optional
All particles within min_edge_dist of the (padded) image
edges are automatically deleted. Default is 2.0
check_rad_cutoff : 2-element list of floats, optional
Particles with radii < check_rad_cutoff[0] or > check_rad_cutoff[1]
are checked if they should be deleted. Set to 'calc' to make it the
median rad +- 3.5 * radius std. Default is [3.5, 15].
check_outside_im : Bool, optional
If True, checks if particles located outside the unpadded image
should be deleted. Default is True.
tries : Int, optional
The maximum number of particles with radii < check_rad_cutoff
to try to remove. Checks in increasing order of radius size.
Default is 50.
im_change_frac : Float, , optional
Number between 0 and 1. If removing a particle decreases the
error by less than im_change_frac*the change in the image, then
the particle is deleted. Default is 0.2
Returns
-------
removed: Int
The cumulative number of particles removed.
"""
is_near_im_edge = lambda pos, pad: (((pos + st.pad) < pad) | (pos >
np.array(st.ishape.shape) + st.pad - pad)).any(axis=1)
# returns True if the position is within 'pad' of the _outer_ image edge
removed = 0
attempts = 0
n_tot_part = st.obj_get_positions().shape[0]
q10 = int(0.1 * n_tot_part) # 10% quartile
r_sig = np.sort(st.obj_get_radii())[q10:-q10].std()
r_med = np.median(st.obj_get_radii())
if max_rad == 'calc':
max_rad = r_med + 15*r_sig
if min_rad == 'calc':
min_rad = r_med - 25*r_sig
if check_rad_cutoff == 'calc':
check_rad_cutoff = [r_med - 7.5*r_sig, r_med + 7.5*r_sig]
# 1. Automatic deletion:
rad_wrong_size = np.nonzero(
(st.obj_get_radii() < min_rad) | (st.obj_get_radii() > max_rad))[0]
near_im_edge = np.nonzero(is_near_im_edge(st.obj_get_positions(),
min_edge_dist - st.pad))[0]
delete_inds = np.unique(np.append(rad_wrong_size, near_im_edge)).tolist()
delete_poses = st.obj_get_positions()[delete_inds].tolist()
message = ('-'*27 + 'SUBTRACTING' + '-'*28 +
'\n Z\t Y\t X\t R\t|\t ERR0\t\t ERR1')
with log.noformat():
CLOG.info(message)
for pos in delete_poses:
ind = st.obj_closest_particle(pos)
old_err = st.error
p, r = st.obj_remove_particle(ind)
p = p[0]
r = r[0]
part_msg = '%2.2f\t%3.2f\t%3.2f\t%3.2f\t|\t%4.3f \t%4.3f' % (
tuple(p) + (r,) + (old_err, st.error))
with log.noformat():
CLOG.info(part_msg)
removed += 1
# 2. Conditional deletion:
check_rad_inds = np.nonzero((st.obj_get_radii() < check_rad_cutoff[0]) |
(st.obj_get_radii() > check_rad_cutoff[1]))[0]
if check_outside_im:
check_edge_inds = np.nonzero(
is_near_im_edge(st.obj_get_positions(), st.pad))[0]
check_inds = np.unique(np.append(check_rad_inds, check_edge_inds))
else:
check_inds = check_rad_inds
check_inds = check_inds[np.argsort(st.obj_get_radii()[check_inds])]
tries = np.min([tries, check_inds.size])
check_poses = st.obj_get_positions()[check_inds[:tries]].copy()
for pos in check_poses:
old_err = st.error
ind = st.obj_closest_particle(pos)
killed, p, r = check_remove_particle(
st, ind, im_change_frac=im_change_frac)
if killed:
removed += 1
check_inds[check_inds > ind] -= 1 # cleaning up indices....
delete_poses.append(pos)
part_msg = '%2.2f\t%3.2f\t%3.2f\t%3.2f\t|\t%4.3f \t%4.3f' % (
p + r + (old_err, st.error))
with log.noformat():
CLOG.info(part_msg)
return removed, delete_poses
|
Automatically adds and subtracts missing & extra particles.
|
def add_subtract(st, max_iter=7, max_npart='calc', max_mem=2e8,
always_check_remove=False, **kwargs):
"""
Automatically adds and subtracts missing & extra particles.
Operates by removing bad particles then adding missing particles on
repeat, until either no particles are added/removed or after `max_iter`
attempts.
Parameters
----------
st: :class:`peri.states.State`
The state to add and subtract particles to.
max_iter : Int, optional
The maximum number of add-subtract loops to use. Default is 7.
Terminates after either max_iter loops or when nothing has changed.
max_npart : Int or 'calc', optional
The maximum number of particles to add before optimizing the non-psf
globals. Default is ``'calc'``, which uses 5% of the initial number
of particles.
max_mem : Int, optional
The maximum memory to use for optimization after adding max_npart
particles. Default is 2e8.
always_check_remove : Bool, optional
Set to True to always check whether to remove particles. If ``False``,
only checks for removal while particles were removed on the previous
attempt. Default is False.
Other Parameters
----------------
invert : Bool, optional
``True`` if the particles are dark on a bright background, ``False``
if they are bright on a dark background. Default is ``True``.
min_rad : Float, optional
Particles with radius below ``min_rad`` are automatically deleted.
Default is ``'calc'`` = median rad - 25* radius std.
max_rad : Float, optional
Particles with radius above ``max_rad`` are automatically deleted.
Default is ``'calc'`` = median rad + 15* radius std, but you should
change this for your particle sizes.
min_edge_dist : Float, optional
Particles closer to the edge of the padded image than this are
automatically deleted. Default is 2.0.
check_rad_cutoff : 2-element float list.
Particles with ``radii < check_rad_cutoff[0]`` or ``> check...[1]``
are checked if they should be deleted (not automatic). Default is
``[3.5, 15]``.
check_outside_im : Bool, optional
Set to True to check whether to delete particles whose positions are
outside the un-padded image.
rad : Float, optional
The initial radius for added particles; added particles radii are
not fit until the end of ``add_subtract``. Default is ``'calc'``,
which uses the median radii of active particles.
tries : Int, optional
The number of particles to attempt to remove or add, per iteration.
Default is 50.
im_change_frac : Float, optional
How good the change in error needs to be relative to the change in
the difference image. Default is 0.2; i.e. if the error does not
decrease by 20% of the change in the difference image, do not add
the particle.
min_derr : Float, optional
The minimum change in the state's error to keep a particle in the
image. Default is ``'3sig'`` which uses ``3*st.sigma``.
do_opt : Bool, optional
Set to False to avoid optimizing particle positions after adding.
minmass : Float, optional
The minimum mass for a particle to be identified as a feature,
as used by trackpy. Defaults to a decent guess.
use_tp : Bool, optional
Set to True to use trackpy to find missing particles inside the
image. Not recommended since trackpy deliberately cuts out particles
at the edge of the image. Default is ``False``.
Returns
-------
total_changed : Int
The total number of adds and subtracts done on the data. Not the
same as ``changed_inds.size`` since the same particle or particle
index can be added/subtracted multiple times.
added_positions : [N_added,3] numpy.ndarray
The positions of particles that have been added at any point in the
add-subtract cycle.
removed_positions : [N_added,3] numpy.ndarray
The positions of particles that have been removed at any point in
the add-subtract cycle.
Notes
------
Occasionally after the intial featuring a cluster of particles is
featured as 1 big particle. To fix these mistakes, it helps to set
max_rad to a physical value. This removes the big particle and allows
it to be re-featured by (several passes of) the adds.
The added/removed positions returned are whether or not the position
has been added or removed ever. It's possible that a position is
added, then removed during a later iteration.
"""
if max_npart == 'calc':
max_npart = 0.05 * st.obj_get_positions().shape[0]
total_changed = 0
_change_since_opt = 0
removed_poses = []
added_poses0 = []
added_poses = []
nr = 1 # Check removal on the first loop
for _ in range(max_iter):
if (nr != 0) or (always_check_remove):
nr, rposes = remove_bad_particles(st, **kwargs)
na, aposes = add_missing_particles(st, **kwargs)
current_changed = na + nr
removed_poses.extend(rposes)
added_poses0.extend(aposes)
total_changed += current_changed
_change_since_opt += current_changed
if current_changed == 0:
break
elif _change_since_opt > max_npart:
_change_since_opt *= 0
CLOG.info('Start add_subtract optimization.')
opt.do_levmarq(st, opt.name_globals(st, remove_params=st.get(
'psf').params), max_iter=1, run_length=4, num_eig_dirs=3,
max_mem=max_mem, eig_update_frequency=2, rz_order=0,
use_accel=True)
CLOG.info('After optimization:\t{:.6}'.format(st.error))
# Optimize the added particles' radii:
for p in added_poses0:
i = st.obj_closest_particle(p)
opt.do_levmarq_particles(st, np.array([i]), max_iter=2, damping=0.3)
added_poses.append(st.obj_get_positions()[i])
return total_changed, np.array(removed_poses), np.array(added_poses)
|
Identifies regions of missing/ misfeatured particles based on the residuals local deviation from uniform Gaussian noise.
|
def identify_misfeatured_regions(st, filter_size=5, sigma_cutoff=8.):
"""
Identifies regions of missing/misfeatured particles based on the
residuals' local deviation from uniform Gaussian noise.
Parameters
----------
st : :class:`peri.states.State`
The state in which to identify mis-featured regions.
filter_size : Int, best if odd.
The size of the filter for calculating the local standard deviation;
should approximately be the size of a poorly featured region in
each dimension. Default is 5.
sigma_cutoff : Float or `otsu`, optional
The max allowed deviation of the residuals from what is expected,
in units of the residuals' standard deviation. Lower means more
sensitive, higher = less sensitive. Default is 8.0, i.e. one pixel
out of every 7*10^11 is mis-identified randomly. In practice the
noise is not Gaussian so there are still some regions mis-identified
as improperly featured. Set to ```otsu``` to calculate this number
based on an automatic Otsu threshold.
Returns
-------
tiles : List of :class:`peri.util.Tile`
Each tile is the smallest bounding tile that contains an improperly
featured region. The list is sorted by the tile's volume.
Notes
-----
Algorithm is
1. Create a field of the local standard deviation, as measured over
a hypercube of size filter_size.
2. Find the maximum reasonable value of the field. [The field should
be a random variable with mean of r.std() and standard deviation
of ~r.std() / sqrt(N), where r is the residuals and N is the
number of pixels in the hypercube.]
3. Label & Identify the misfeatured regions as portions where
the local error is too large.
4. Parse the misfeatured regions into tiles.
5. Return the sorted tiles.
The Otsu option to calculate the sigma cutoff works well for images
that actually contain missing particles, returning a number similar
to one calculated with a sigma cutoff. However, if the image is
well-featured with Gaussian residuals, then the Otsu threshold
splits the Gaussian down the middle instead of at the tails, which
is very bad. So use with caution.
"""
# 1. Field of local std
r = st.residuals
weights = np.ones([filter_size]*len(r.shape), dtype='float')
weights /= weights.sum()
f = np.sqrt(nd.filters.convolve(r*r, weights, mode='reflect'))
# 2. Maximal reasonable value of the field.
if sigma_cutoff == 'otsu':
max_ok = initializers.otsu_threshold(f)
else:
# max_ok = f.mean() * (1 + sigma_cutoff / np.sqrt(weights.size))
max_ok = f.mean() + sigma_cutoff * f.std()
# 3. Label & Identify
bad = f > max_ok
labels, n = nd.measurements.label(bad)
inds = []
for i in range(1, n+1):
inds.append(np.nonzero(labels == i))
# 4. Parse into tiles
tiles = [Tile(np.min(ind, axis=1), np.max(ind, axis=1)+1) for ind in inds]
# 5. Sort and return
volumes = [t.volume for t in tiles]
return [tiles[i] for i in np.argsort(volumes)[::-1]]
|
Automatically adds and subtracts missing & extra particles in a region of poor fit.
|
def add_subtract_misfeatured_tile(
st, tile, rad='calc', max_iter=3, invert='guess', max_allowed_remove=20,
minmass=None, use_tp=False, **kwargs):
"""
Automatically adds and subtracts missing & extra particles in a region
of poor fit.
Parameters
----------
st: :class:`peri.states.State`
The state to add and subtract particles to.
tile : :class:`peri.util.Tile`
The poorly-fit region to examine.
rad : Float or 'calc', optional
The initial radius for added particles; added particles radii are
not fit until the end of add_subtract. Default is ``'calc'``, which
uses the median radii of active particles.
max_iter : Int, optional
The maximum number of loops for attempted adds at one tile location.
Default is 3.
invert : {'guess', True, False}, optional
Whether to invert the image for feature_guess -- True for dark
particles on a bright background, False for bright particles. The
default is to guess from the state's current particles.
max_allowed_remove : Int, optional
The maximum number of particles to remove. If the misfeatured tile
contains more than this many particles, raises an error. If it
contains more than half as many particles, logs a warning. If more
than this many particles are added, they are optimized in blocks of
``max_allowed_remove``. Default is 20.
Other Parameters
----------------
im_change_frac : Float on [0, 1], optional.
If adding or removing a particle decreases the error less than
``im_change_frac``*the change in the image, the particle is deleted.
Default is 0.2.
min_derr : {Float, ``'3sig'``}, optional
The minimum change in the state's error to keep a particle in the
image. Default is ``'3sig'`` which uses ``3*st.sigma``.
do_opt : Bool, optional
Set to False to avoid optimizing particle positions after adding
them. Default is True.
minmass : Float, optional
The minimum mass for a particle to be identified as a feature, as
used by trackpy. Defaults to a decent guess.
use_tp : Bool, optional
Set to True to use trackpy to find missing particles inside the
image. Not recommended since trackpy deliberately cuts out particles
at the edge of the image. Default is False.
Outputs
-------
n_added : Int
The change in the number of particles, i.e. ``n_added-n_subtracted``
ainds: List of ints
The indices of the added particles.
Notes
--------
The added/removed positions returned are whether or not the
position has been added or removed ever. It's possible/probably that
a position is added, then removed during a later iteration.
Algorithm is:
1. Remove all particles within the tile.
2. Feature and add particles to the tile.
3. Optimize the added particles positions only.
4. Run 2-3 until no particles have been added.
5. Optimize added particle radii
Because all the particles are removed within a tile, it is important
to set max_allowed_remove to a reasonable value. Otherwise, if the
tile is the size of the image it can take a long time to remove all
the particles and re-add them.
"""
if rad == 'calc':
rad = guess_add_radii(st)
if invert == 'guess':
invert = guess_invert(st)
# 1. Remove all possibly bad particles within the tile.
initial_error = np.copy(st.error)
rinds = np.nonzero(tile.contains(st.obj_get_positions()))[0]
if rinds.size >= max_allowed_remove:
CLOG.fatal('Misfeatured region too large!')
raise RuntimeError
elif rinds.size >= max_allowed_remove/2:
CLOG.warn('Large misfeatured regions.')
elif rinds.size > 0:
rpos, rrad = st.obj_remove_particle(rinds)
# 2-4. Feature & add particles to the tile, optimize, run until none added
n_added = -rinds.size
added_poses = []
for _ in range(max_iter):
if invert:
im = 1 - st.residuals[tile.slicer]
else:
im = st.residuals[tile.slicer]
guess, _ = _feature_guess(im, rad, minmass=minmass, use_tp=use_tp)
accepts, poses = check_add_particles(
st, guess+tile.l, rad=rad, do_opt=True, **kwargs)
added_poses.extend(poses)
n_added += accepts
if accepts == 0:
break
else: # for-break-else
CLOG.warn('Runaway adds or insufficient max_iter')
# 5. Optimize added pos + rad:
ainds = []
for p in added_poses:
ainds.append(st.obj_closest_particle(p))
if len(ainds) > max_allowed_remove:
for i in range(0, len(ainds), max_allowed_remove):
opt.do_levmarq_particles(
st, np.array(ainds[i:i + max_allowed_remove]),
include_rad=True, max_iter=3)
elif len(ainds) > 0:
opt.do_levmarq_particles(st, ainds, include_rad=True, max_iter=3)
# 6. Ensure that current error after add-subtracting is lower than initial
did_something = (rinds.size > 0) or (len(ainds) > 0)
if did_something & (st.error > initial_error):
CLOG.info('Failed addsub, Tile {} -> {}'.format(
tile.l.tolist(), tile.r.tolist()))
if len(ainds) > 0:
_ = st.obj_remove_particle(ainds)
if rinds.size > 0:
for p, r in zip(rpos.reshape(-1, 3), rrad.reshape(-1)):
_ = st.obj_add_particle(p, r)
n_added = 0
ainds = []
return n_added, ainds
|
Automatically adds and subtracts missing particles based on local regions of poor fit.
|
def add_subtract_locally(st, region_depth=3, filter_size=5, sigma_cutoff=8,
**kwargs):
"""
Automatically adds and subtracts missing particles based on local
regions of poor fit.
Calls identify_misfeatured_regions to identify regions, then
add_subtract_misfeatured_tile on the tiles in order of size until
region_depth tiles have been checked without adding any particles.
Parameters
----------
st: :class:`peri.states.State`
The state to add and subtract particles to.
region_depth : Int
The minimum amount of regions to try; the algorithm terminates if
region_depth regions have been tried without adding particles.
Other Parameters
----------------
filter_size : Int, optional
The size of the filter for calculating the local standard deviation;
should approximately be the size of a poorly featured region in each
dimension. Best if odd. Default is 5.
sigma_cutoff : Float, optional
The max allowed deviation of the residuals from what is expected,
in units of the residuals' standard deviation. Lower means more
sensitive, higher = less sensitive. Default is 8.0, i.e. one pixel
out of every ``7*10^11`` is mis-identified randomly. In practice the
noise is not Gaussian so there are still some regions mis-
identified as improperly featured.
rad : Float or 'calc', optional
The initial radius for added particles; added particles radii are
not fit until the end of add_subtract. Default is ``'calc'``, which
uses the median radii of active particles.
max_iter : Int, optional
The maximum number of loops for attempted adds at one tile location.
Default is 3.
invert : Bool, optional
Whether to invert the image for feature_guess. Default is ``True``,
i.e. dark particles on bright background.
max_allowed_remove : Int, optional
The maximum number of particles to remove. If the misfeatured tile
contains more than this many particles, raises an error. If it
contains more than half as many particles, throws a warning. If more
than this many particles are added, they are optimized in blocks of
``max_allowed_remove``. Default is 20.
im_change_frac : Float, between 0 and 1.
If adding or removing a particle decreases the error less than
``im_change_frac *`` the change in the image, the particle is deleted.
Default is 0.2.
min_derr : Float
The minimum change in the state's error to keep a particle in the
image. Default is ``'3sig'`` which uses ``3*st.sigma``.
do_opt : Bool, optional
Set to False to avoid optimizing particle positions after adding
them. Default is True
minmass : Float, optional
The minimum mass for a particle to be identified as a feature, as
used by trackpy. Defaults to a decent guess.
use_tp : Bool, optional
Set to True to use trackpy to find missing particles inside the
image. Not recommended since trackpy deliberately cuts out
particles at the edge of the image. Default is False.
max_allowed_remove : Int, optional
The maximum number of particles to remove. If the misfeatured tile
contains more than this many particles, raises an error. If it
contains more than half as many particles, throws a warning. If more
than this many particles are added, they are optimized in blocks of
``max_allowed_remove``. Default is 20.
Returns
-------
n_added : Int
The change in the number of particles; i.e the number added - number
removed.
new_poses : List
[N,3] element list of the added particle positions.
Notes
-----
Algorithm Description
1. Identify mis-featured regions by how much the local residuals
deviate from the global residuals, as measured by the standard
deviation of both.
2. Loop over each of those regions, and:
a. Remove every particle in the current region.
b. Try to add particles in the current region until no more
can be added while adequately decreasing the error.
c. Terminate if at least region_depth regions have been
checked without successfully adding a particle.
Because this algorithm is more judicious about chooosing regions to
check, and more aggressive about removing particles in those regions,
it runs faster and does a better job than the (global) add_subtract.
However, this function usually does not work better as an initial add-
subtract on an image, since (1) it doesn't check for removing small/big
particles per se, and (2) when the poorly-featured regions of the image
are large or when the fit is bad, it will remove essentially all of the
particles, taking a long time. As a result, it's usually best to do a
normal add_subtract first and using this function for tough missing or
double-featured particles.
"""
# 1. Find regions of poor tiles:
tiles = identify_misfeatured_regions(
st, filter_size=filter_size, sigma_cutoff=sigma_cutoff)
# 2. Add and subtract in the regions:
n_empty = 0
n_added = 0
new_poses = []
for t in tiles:
curn, curinds = add_subtract_misfeatured_tile(st, t, **kwargs)
if curn == 0:
n_empty += 1
else:
n_added += curn
new_poses.extend(st.obj_get_positions()[curinds])
if n_empty > region_depth:
break # some message or something?
else: # for-break-else
pass
# CLOG.info('All regions contained particles.')
# something else?? this is not quite true
return n_added, new_poses
|
Guesses whether particles are bright on a dark bkg or vice - versa
|
def guess_invert(st):
"""Guesses whether particles are bright on a dark bkg or vice-versa
Works by checking whether the intensity at the particle centers is
brighter or darker than the average intensity of the image, by
comparing the median intensities of each.
Parameters
----------
st : :class:`peri.states.ImageState`
Returns
-------
invert : bool
Whether to invert the image for featuring.
"""
pos = st.obj_get_positions()
pxinds_ar = np.round(pos).astype('int')
inim = st.ishape.translate(-st.pad).contains(pxinds_ar)
pxinds_tuple = tuple(pxinds_ar[inim].T)
pxvals = st.data[pxinds_tuple]
invert = np.median(pxvals) < np.median(st.data) # invert if dark particles
return invert
|
Prime FFTW with knowledge of which FFTs are best on this machine by loading wisdom from the file wisdomfile
|
def load_wisdom(wisdomfile):
"""
Prime FFTW with knowledge of which FFTs are best on this machine by
loading 'wisdom' from the file ``wisdomfile``
"""
if wisdomfile is None:
return
try:
pyfftw.import_wisdom(pickle.load(open(wisdomfile, 'rb')))
except (IOError, TypeError) as e:
log.warn("No wisdom present, generating some at %r" % wisdomfile)
save_wisdom(wisdomfile)
|
Save the acquired wisdom generated by FFTW to file so that future initializations of FFTW will be faster.
|
def save_wisdom(wisdomfile):
"""
Save the acquired 'wisdom' generated by FFTW to file so that future
initializations of FFTW will be faster.
"""
if wisdomfile is None:
return
if wisdomfile:
pickle.dump(
pyfftw.export_wisdom(), open(wisdomfile, 'wb'),
protocol=2
)
|
How much of inner is in outer by volume
|
def tile_overlap(inner, outer, norm=False):
""" How much of inner is in outer by volume """
div = 1.0/inner.volume if norm else 1.0
return div*(inner.volume - util.Tile.intersection(inner, outer).volume)
|
Given a tiling of space ( by state shift and size ) find the closest tile to another external tile
|
def closest_uniform_tile(s, shift, size, other):
"""
Given a tiling of space (by state, shift, and size), find the closest
tile to another external tile
"""
region = util.Tile(size, dim=s.dim, dtype='float').translate(shift - s.pad)
vec = np.round((other.center - region.center) / region.shape)
return region.translate(region.shape * vec)
|
Given a state returns a list of groups of particles. Each group of particles are located near each other in the image. Every particle located in the desired region is contained in exactly 1 group.
|
def separate_particles_into_groups(s, region_size=40, bounds=None):
"""
Given a state, returns a list of groups of particles. Each group of
particles are located near each other in the image. Every particle
located in the desired region is contained in exactly 1 group.
Parameters:
-----------
s : state
The PERI state to find particles in.
region_size: int or list of ints
The size of the box. Groups particles into boxes of shape region_size.
If region_size is a scalar, the box is a cube of length region_size.
Default is 40.
bounds: 2-element list-like of 3-element lists.
The sub-region of the image over which to look for particles.
bounds[0]: The lower-left corner of the image region.
bounds[1]: The upper-right corner of the image region.
Default (None -> ([0,0,0], s.oshape.shape)) is a box of the entire
image size, i.e. the default places every particle in the image
somewhere in the groups.
Returns:
-----------
particle_groups: list
Each element of particle_groups is an int numpy.ndarray of the
group of nearby particles. Only contains groups with a nonzero
number of particles, so the elements don't necessarily correspond
to a given image region.
"""
imtile = (
s.oshape.translate(-s.pad) if bounds is None else
util.Tile(bounds[0], bounds[1])
)
# does all particle including out of image, is that correct?
region = util.Tile(region_size, dim=s.dim)
trange = np.ceil(imtile.shape.astype('float') / region.shape)
translations = util.Tile(trange).coords(form='vector')
translations = translations.reshape(-1, translations.shape[-1])
groups = []
positions = s.obj_get_positions()
for v in translations:
tmptile = region.copy().translate(region.shape * v - s.pad)
groups.append(find_particles_in_tile(positions, tmptile))
return [g for g in groups if len(g) > 0]
|
Take a platonic image and position and create a state which we can use to sample the error for peri. Also return the blurred platonic image so we can vary the noise on it later
|
def create_comparison_state(image, position, radius=5.0, snr=20,
method='constrained-cubic', extrapad=2, zscale=1.0):
"""
Take a platonic image and position and create a state which we can
use to sample the error for peri. Also return the blurred platonic
image so we can vary the noise on it later
"""
# first pad the image slightly since they are pretty small
image = common.pad(image, extrapad, 0)
# place that into a new image at the expected parameters
s = init.create_single_particle_state(imsize=np.array(image.shape), sigma=1.0/snr,
radius=radius, psfargs={'params': np.array([2.0, 1.0, 3.0]), 'error': 1e-6, 'threads': 2},
objargs={'method': method}, stateargs={'sigmapad': False, 'pad': 4, 'zscale': zscale})
s.obj.pos[0] = position + s.pad + extrapad
s.reset()
s.model_to_true_image()
timage = 1-np.pad(image, s.pad, mode='constant', constant_values=0)
timage = s.psf.execute(timage)
return s, timage[s.inner]
|
platonics = create_many_platonics ( N = 50 ) dorun ( platonics )
|
def dorun(method, platonics=None, nsnrs=20, noise_samples=30, sweeps=30, burn=15):
"""
platonics = create_many_platonics(N=50)
dorun(platonics)
"""
sigmas = np.logspace(np.log10(1.0/2048), 0, nsnrs)
crbs, vals, errs, poss = [], [], [], []
for sigma in sigmas:
print "#### sigma:", sigma
for i, (image, pos) in enumerate(platonics):
print 'image', i, '|',
s,im = create_comparison_state(image, pos, method=method)
# typical image
set_image(s, im, sigma)
crbs.append(crb(s))
val, err = sample(s, im, sigma, N=noise_samples, sweeps=sweeps, burn=burn)
poss.append(pos)
vals.append(val)
errs.append(err)
shape0 = (nsnrs, len(platonics), -1)
shape1 = (nsnrs, len(platonics), noise_samples, -1)
crbs = np.array(crbs).reshape(shape0)
vals = np.array(vals).reshape(shape1)
errs = np.array(errs).reshape(shape1)
poss = np.array(poss).reshape(shape0)
return [crbs, vals, errs, poss, sigmas]
|
Create a perfect platonic sphere of a given radius R by supersampling by a factor scale on a grid of size N. Scale must be odd.
|
def perfect_platonic_per_pixel(N, R, scale=11, pos=None, zscale=1.0, returnpix=None):
"""
Create a perfect platonic sphere of a given radius R by supersampling by a
factor scale on a grid of size N. Scale must be odd.
We are able to perfectly position these particles up to 1/scale. Therefore,
let's only allow those types of shifts for now, but return the actual position
used for the placement.
"""
# enforce odd scale size
if scale % 2 != 1:
scale += 1
if pos is None:
# place the default position in the center of the grid
pos = np.array([(N-1)/2.0]*3)
# limit positions to those that are exact on the size 1./scale
# positions have the form (d = divisions):
# p = N + m/d
s = 1.0/scale
f = zscale**2
i = pos.astype('int')
p = i + s*((pos - i)/s).astype('int')
pos = p + 1e-10 # unfortunately needed to break ties
# make the output arrays
image = np.zeros((N,)*3)
x,y,z = np.meshgrid(*(xrange(N),)*3, indexing='ij')
# for each real pixel in the image, integrate a bunch of superres pixels
for x0,y0,z0 in zip(x.flatten(),y.flatten(),z.flatten()):
# short-circuit things that are just too far away!
ddd = np.sqrt(f*(x0-pos[0])**2 + (y0-pos[1])**2 + (z0-pos[2])**2)
if ddd > R + 4:
image[x0,y0,z0] = 0.0
continue
# otherwise, build the local mesh and count the volume
xp,yp,zp = np.meshgrid(
*(np.linspace(i-0.5+s/2, i+0.5-s/2, scale, endpoint=True) for i in (x0,y0,z0)),
indexing='ij'
)
ddd = np.sqrt(f*(xp-pos[0])**2 + (yp-pos[1])**2 + (zp-pos[2])**2)
if returnpix is not None and returnpix == [x0,y0,z0]:
outpix = 1.0 * (ddd < R)
vol = (1.0*(ddd < R) + 0.0*(ddd == R)).sum()
image[x0,y0,z0] = vol / float(scale**3)
#vol_true = 4./3*np.pi*R**3
#vol_real = image.sum()
#print vol_true, vol_real, (vol_true - vol_real)/vol_true
if returnpix:
return image, pos, outpix
return image, pos
|
Translate an image in fourier - space with plane waves
|
def translate_fourier(image, dx):
""" Translate an image in fourier-space with plane waves """
N = image.shape[0]
f = 2*np.pi*np.fft.fftfreq(N)
kx,ky,kz = np.meshgrid(*(f,)*3, indexing='ij')
kv = np.array([kx,ky,kz]).T
q = np.fft.fftn(image)*np.exp(-1.j*(kv*dx).sum(axis=-1)).T
return np.real(np.fft.ifftn(q))
|
Standardizing the plot format of the does_matter section. See any of the accompaning files to see how to use this generalized plot.
|
def doplot(image0, image1, xs, crbs, errors, labels, diff_image_scale=0.1,
dolabels=True, multiple_crbs=True, xlim=None, ylim=None, highlight=None,
detailed_labels=False, xlabel="", title=""):
"""
Standardizing the plot format of the does_matter section. See any of the
accompaning files to see how to use this generalized plot.
image0 : ground true
image1 : difference image
xs : list of x values for the plots
crbs : list of lines of values of the crbs
errors : list of lines of errors
labels : legend labels for each curve
"""
if len(crbs) != len(errors) or len(crbs) != len(labels):
raise IndexError, "lengths are not consistent"
fig = pl.figure(figsize=(14,7))
ax = fig.add_axes([0.43, 0.15, 0.52, 0.75])
gs = ImageGrid(fig, rect=[0.05, 0.05, 0.25, 0.90], nrows_ncols=(2,1), axes_pad=0.25,
cbar_location='right', cbar_mode='each', cbar_size='10%', cbar_pad=0.04)
diffm = diff_image_scale*np.ceil(np.abs(image1).max()/diff_image_scale)
im0 = gs[0].imshow(image0, vmin=0, vmax=1, cmap='bone_r')
im1 = gs[1].imshow(image1, vmin=-diffm, vmax=diffm, cmap='RdBu')
cb0 = pl.colorbar(im0, cax=gs[0].cax, ticks=[0,1])
cb1 = pl.colorbar(im1, cax=gs[1].cax, ticks=[-diffm,diffm])
cb0.ax.set_yticklabels(['0', '1'])
cb1.ax.set_yticklabels(['-%0.1f' % diffm, '%0.1f' % diffm])
image_names = ["Reference", "Difference"]
for i in xrange(2):
gs[i].set_xticks([])
gs[i].set_yticks([])
gs[i].set_ylabel(image_names[i])
if dolabels:
lbl(gs[i], figlbl[i])
symbols = ['o', '^', 'D', '>']
for i in xrange(len(labels)):
c = COLORS[i]
if multiple_crbs or i == 0:
if multiple_crbs:
label = labels[i] if (i != 0 and not detailed_labels) else '%s CRB' % labels[i]
else:
label = 'CRB'
ax.plot(xs[i], crbs[i], '-', c=c, lw=3, label=label)
label = labels[i] if (i != 0 and not detailed_labels) else '%s Error' % labels[i]
ax.plot(xs[i], errors[i], symbols[i], ls='--', lw=2, c=c, label=label, ms=12)
if dolabels:
lbl(ax, 'D')
ax.loglog()
if xlim:
ax.set_xlim(xlim)
if ylim:
ax.set_ylim(ylim)
ax.legend(loc='upper left', ncol=2, prop={'size': 18}, numpoints=1)
ax.set_xlabel(xlabel)
ax.set_ylabel(r"Position CRB, Error")
ax.grid(False, which='both', axis='both')
ax.set_title(title)
return gs, ax
|
Load default users and groups.
|
def users():
"""Load default users and groups."""
from invenio_groups.models import Group, Membership, \
PrivacyPolicy, SubscriptionPolicy
admin = accounts.datastore.create_user(
email='admin@inveniosoftware.org',
password=encrypt_password('123456'),
active=True,
)
reader = accounts.datastore.create_user(
email='reader@inveniosoftware.org',
password=encrypt_password('123456'),
active=True,
)
admins = Group.create(name='admins', admins=[admin])
for i in range(10):
Group.create(name='group-{0}'.format(i), admins=[admin])
Membership.create(admins, reader)
db.session.commit()
|
# This is equivalent for i in range ( self. N - 1 ): for j in range ( i + 1 self. N ): d = (( self. zscale * ( self. pos [ i ] - self. pos [ j ] )) ** 2 ). sum ( axis = - 1 ) r = ( self. rad [ i ] + self. rad [ j ] ) ** 2
|
def _calculate(self):
self.logpriors = np.zeros_like(self.rad)
for i in range(self.N-1):
o = np.arange(i+1, self.N)
dist = ((self.zscale*(self.pos[i] - self.pos[o]))**2).sum(axis=-1)
dist0 = (self.rad[i] + self.rad[o])**2
update = self.prior_func(dist - dist0)
self.logpriors[i] += np.sum(update)
self.logpriors[o] += update
"""
# This is equivalent
for i in range(self.N-1):
for j in range(i+1, self.N):
d = ((self.zscale*(self.pos[i] - self.pos[j]))**2).sum(axis=-1)
r = (self.rad[i] + self.rad[j])**2
cost = self.prior_func(d - r)
self.logpriors[i] += cost
self.logpriors[j] += cost
"""
|
weighting function for Barnes
|
def _weight(self, rsq, sigma=None):
"""weighting function for Barnes"""
sigma = sigma or self.filter_size
if not self.clip:
o = np.exp(-rsq / (2*sigma**2))
else:
o = np.zeros(rsq.shape, dtype='float')
m = (rsq < self.clipsize**2)
o[m] = np.exp(-rsq[m] / (2*sigma**2))
return o
|
The first - order Barnes approximation
|
def _eval_firstorder(self, rvecs, data, sigma):
"""The first-order Barnes approximation"""
if not self.blocksize:
dist_between_points = self._distance_matrix(rvecs, self.x)
gaussian_weights = self._weight(dist_between_points, sigma=sigma)
return gaussian_weights.dot(data) / gaussian_weights.sum(axis=1)
else:
# Now rather than calculating the distance matrix all at once,
# we do it in chunks over rvecs
ans = np.zeros(rvecs.shape[0], dtype='float')
bs = self.blocksize
for a in range(0, rvecs.shape[0], bs):
dist = self._distance_matrix(rvecs[a:a+bs], self.x)
weights = self._weight(dist, sigma=sigma)
ans[a:a+bs] += weights.dot(data) / weights.sum(axis=1)
return ans
|
Correct normalized version of Barnes
|
def _newcall(self, rvecs):
"""Correct, normalized version of Barnes"""
# 1. Initial guess for output:
sigma = 1*self.filter_size
out = self._eval_firstorder(rvecs, self.d, sigma)
# 2. There are differences between 0th order at the points and
# the passed data, so we iterate to remove:
ondata = self._eval_firstorder(self.x, self.d, sigma)
for i in range(self.iterations):
out += self._eval_firstorder(rvecs, self.d-ondata, sigma)
ondata += self._eval_firstorder(self.x, self.d-ondata, sigma)
sigma *= self.damp
return out
|
Barnes w/ o normalizing the weights
|
def _oldcall(self, rvecs):
"""Barnes w/o normalizing the weights"""
g = self.filter_size
dist0 = self._distance_matrix(self.x, self.x)
dist1 = self._distance_matrix(rvecs, self.x)
tmp = self._weight(dist0, g).dot(self.d)
out = self._weight(dist1, g).dot(self.d)
for i in range(self.iterations):
out = out + self._weight(dist1, g).dot(self.d - tmp)
tmp = tmp + self._weight(dist0, g).dot(self.d - tmp)
g *= self.damp
return out
|
Pairwise distance between each point in a and each point in b
|
def _distance_matrix(self, a, b):
"""Pairwise distance between each point in `a` and each point in `b`"""
def sq(x): return (x * x)
# matrix = np.sum(map(lambda a,b: sq(a[:,None] - b[None,:]), a.T,
# b.T), axis=0)
# A faster version than above:
matrix = sq(a[:, 0][:, None] - b[:, 0][None, :])
for x, y in zip(a.T[1:], b.T[1:]):
matrix += sq(x[:, None] - y[None, :])
return matrix
|
Convert windowdow coordinates to cheb coordinates [ - 1 1 ]
|
def _x2c(self, x):
""" Convert windowdow coordinates to cheb coordinates [-1,1] """
return ((2 * x - self.window[1] - self.window[0]) /
(self.window[1] - self.window[0]))
|
Convert cheb coordinates to windowdow coordinates
|
def _c2x(self, c):
""" Convert cheb coordinates to windowdow coordinates """
return 0.5 * (self.window[0] + self.window[1] +
c * (self.window[1] - self.window[0]))
|
Calculate the coefficients based on the func degree and interpolating points. _coeffs is a [ order N M.... ] array
|
def _construct_coefficients(self):
"""Calculate the coefficients based on the func, degree, and
interpolating points.
_coeffs is a [order, N,M,....] array
Notes
-----
Moved the -c0 to the coefficients defintion
app -= 0.5 * self._coeffs[0] -- moving this to the coefficients
"""
coeffs = [0]*self.degree
N = float(self.evalpts)
lvals = np.arange(self.evalpts).astype('float')
xpts = self._c2x(np.cos(np.pi*(lvals + 0.5)/N))
fpts = np.rollaxis(self.func(xpts, *self.args), -1)
for a in range(self.degree):
inner = [
fpts[b] * np.cos(np.pi*a*(lvals[b]+0.5)/N)
for b in range(self.evalpts)
]
coeffs[a] = 2.0/N * np.sum(inner, axis=0)
coeffs[0] *= 0.5
self._coeffs = np.array(coeffs)
|
Evaluates an individual Chebyshev polynomial k in coordinate space with proper transformation given the window
|
def tk(self, k, x):
"""
Evaluates an individual Chebyshev polynomial `k` in coordinate space
with proper transformation given the window
"""
weights = np.diag(np.ones(k+1))[k]
return np.polynomial.chebyshev.chebval(self._x2c(x), weights)
|
Determine admin type.
|
def resolve_admin_type(admin):
"""Determine admin type."""
if admin is current_user or isinstance(admin, UserMixin):
return 'User'
else:
return admin.__class__.__name__
|
Validate subscription policy value.
|
def validate(cls, policy):
"""Validate subscription policy value."""
return policy in [cls.OPEN, cls.APPROVAL, cls.CLOSED]
|
Validate privacy policy value.
|
def validate(cls, policy):
"""Validate privacy policy value."""
return policy in [cls.PUBLIC, cls.MEMBERS, cls.ADMINS]
|
Validate state value.
|
def validate(cls, state):
"""Validate state value."""
return state in [cls.ACTIVE, cls.PENDING_ADMIN, cls.PENDING_USER]
|
Create a new group.
|
def create(cls, name=None, description='', privacy_policy=None,
subscription_policy=None, is_managed=False, admins=None):
"""Create a new group.
:param name: Name of group. Required and must be unique.
:param description: Description of group. Default: ``''``
:param privacy_policy: PrivacyPolicy
:param subscription_policy: SubscriptionPolicy
:param admins: list of user and/or group objects. Default: ``[]``
:returns: Newly created group
:raises: IntegrityError: if group with given name already exists
"""
assert name
assert privacy_policy is None or PrivacyPolicy.validate(privacy_policy)
assert subscription_policy is None or \
SubscriptionPolicy.validate(subscription_policy)
assert admins is None or isinstance(admins, list)
with db.session.begin_nested():
obj = cls(
name=name,
description=description,
privacy_policy=privacy_policy,
subscription_policy=subscription_policy,
is_managed=is_managed,
)
db.session.add(obj)
for a in admins or []:
db.session.add(GroupAdmin(
group=obj, admin_id=a.get_id(),
admin_type=resolve_admin_type(a)))
return obj
|
Delete a group and all associated memberships.
|
def delete(self):
"""Delete a group and all associated memberships."""
with db.session.begin_nested():
Membership.query_by_group(self).delete()
GroupAdmin.query_by_group(self).delete()
GroupAdmin.query_by_admin(self).delete()
db.session.delete(self)
|
Update group.
|
def update(self, name=None, description=None, privacy_policy=None,
subscription_policy=None, is_managed=None):
"""Update group.
:param name: Name of group.
:param description: Description of group.
:param privacy_policy: PrivacyPolicy
:param subscription_policy: SubscriptionPolicy
:returns: Updated group
"""
with db.session.begin_nested():
if name is not None:
self.name = name
if description is not None:
self.description = description
if (
privacy_policy is not None and
PrivacyPolicy.validate(privacy_policy)
):
self.privacy_policy = privacy_policy
if (
subscription_policy is not None and
SubscriptionPolicy.validate(subscription_policy)
):
self.subscription_policy = subscription_policy
if is_managed is not None:
self.is_managed = is_managed
db.session.merge(self)
return self
|
Query group by a group name.
|
def get_by_name(cls, name):
"""Query group by a group name.
:param name: Name of a group to search for.
:returns: Group object or None.
"""
try:
return cls.query.filter_by(name=name).one()
except NoResultFound:
return None
|
Query group by a list of group names.
|
def query_by_names(cls, names):
"""Query group by a list of group names.
:param list names: List of the group names.
:returns: Query object.
"""
assert isinstance(names, list)
return cls.query.filter(cls.name.in_(names))
|
Query group by user.
|
def query_by_user(cls, user, with_pending=False, eager=False):
"""Query group by user.
:param user: User object.
:param bool with_pending: Whether to include pending users.
:param bool eager: Eagerly fetch group members.
:returns: Query object.
"""
q1 = Group.query.join(Membership).filter_by(user_id=user.get_id())
if not with_pending:
q1 = q1.filter_by(state=MembershipState.ACTIVE)
if eager:
q1 = q1.options(joinedload(Group.members))
q2 = Group.query.join(GroupAdmin).filter_by(
admin_id=user.get_id(), admin_type=resolve_admin_type(user))
if eager:
q2 = q2.options(joinedload(Group.members))
query = q1.union(q2).with_entities(Group.id)
return Group.query.filter(Group.id.in_(query))
|
Modify query as so include only specific group names.
|
def search(cls, query, q):
"""Modify query as so include only specific group names.
:param query: Query object.
:param str q: Search string.
:returs: Query object.
"""
return query.filter(Group.name.like('%{0}%'.format(q)))
|
Invite a user to a group.
|
def add_member(self, user, state=MembershipState.ACTIVE):
"""Invite a user to a group.
:param user: User to be added as a group member.
:param state: MembershipState. Default: MembershipState.ACTIVE.
:returns: Membership object or None.
"""
return Membership.create(self, user, state)
|
Invite a user to a group ( should be done by admins ).
|
def invite(self, user, admin=None):
"""Invite a user to a group (should be done by admins).
Wrapper around ``add_member()`` to ensure proper membership state.
:param user: User to invite.
:param admin: Admin doing the action. If provided, user is only invited
if the object is an admin for this group. Default: None.
:returns: Newly created Membership or None.
"""
if admin is None or self.is_admin(admin):
return self.add_member(user, state=MembershipState.PENDING_USER)
return None
|
Invite users to a group by emails.
|
def invite_by_emails(self, emails):
"""Invite users to a group by emails.
:param list emails: Emails of users that shall be invited.
:returns list: Newly created Memberships or Nones.
"""
assert emails is None or isinstance(emails, list)
results = []
for email in emails:
try:
user = User.query.filter_by(email=email).one()
results.append(self.invite(user))
except NoResultFound:
results.append(None)
return results
|
Subscribe a user to a group ( done by users ).
|
def subscribe(self, user):
"""Subscribe a user to a group (done by users).
Wrapper around ``add_member()`` which checks subscription policy.
:param user: User to subscribe.
:returns: Newly created Membership or None.
"""
if self.subscription_policy == SubscriptionPolicy.OPEN:
return self.add_member(user)
elif self.subscription_policy == SubscriptionPolicy.APPROVAL:
return self.add_member(user, state=MembershipState.PENDING_ADMIN)
elif self.subscription_policy == SubscriptionPolicy.CLOSED:
return None
|
Verify if given user is a group member.
|
def is_member(self, user, with_pending=False):
"""Verify if given user is a group member.
:param user: User to be checked.
:param bool with_pending: Whether to include pending users or not.
:returns: True or False.
"""
m = Membership.get(self, user)
if m is not None:
if with_pending:
return True
elif m.state == MembershipState.ACTIVE:
return True
return False
|
Determine if given user can see other group members.
|
def can_see_members(self, user):
"""Determine if given user can see other group members.
:param user: User to be checked.
:returns: True or False.
"""
if self.privacy_policy == PrivacyPolicy.PUBLIC:
return True
elif self.privacy_policy == PrivacyPolicy.MEMBERS:
return self.is_member(user) or self.is_admin(user)
elif self.privacy_policy == PrivacyPolicy.ADMINS:
return self.is_admin(user)
|
Determine if user can invite people to a group.
|
def can_invite_others(self, user):
"""Determine if user can invite people to a group.
Be aware that this check is independent from the people (users) which
are going to be invited. The checked user is the one who invites
someone, NOT who is going to be invited.
:param user: User to be checked.
:returns: True or False.
"""
if self.is_managed:
return False
elif self.is_admin(user):
return True
elif self.subscription_policy != SubscriptionPolicy.CLOSED:
return True
else:
return False
|
Get membership for given user and group.
|
def get(cls, group, user):
"""Get membership for given user and group.
:param group: Group object.
:param user: User object.
:returns: Membership or None.
"""
try:
m = cls.query.filter_by(user_id=user.get_id(), group=group).one()
return m
except Exception:
return None
|
Filter a query result.
|
def _filter(cls, query, state=MembershipState.ACTIVE, eager=None):
"""Filter a query result."""
query = query.filter_by(state=state)
eager = eager or []
for field in eager:
query = query.options(joinedload(field))
return query
|
Get a user s memberships.
|
def query_by_user(cls, user, **kwargs):
"""Get a user's memberships."""
return cls._filter(
cls.query.filter_by(user_id=user.get_id()),
**kwargs
)
|
Get all invitations for given user.
|
def query_invitations(cls, user, eager=False):
"""Get all invitations for given user."""
if eager:
eager = [Membership.group]
return cls.query_by_user(user, state=MembershipState.PENDING_USER,
eager=eager)
|
Get all pending group requests.
|
def query_requests(cls, admin, eager=False):
"""Get all pending group requests."""
# Get direct pending request
if hasattr(admin, 'is_superadmin') and admin.is_superadmin:
q1 = GroupAdmin.query.with_entities(
GroupAdmin.group_id)
else:
q1 = GroupAdmin.query_by_admin(admin).with_entities(
GroupAdmin.group_id)
q2 = Membership.query.filter(
Membership.state == MembershipState.PENDING_ADMIN,
Membership.id_group.in_(q1),
)
# Get request from admin groups your are member of
q3 = Membership.query_by_user(
user=admin, state=MembershipState.ACTIVE
).with_entities(Membership.id_group)
q4 = GroupAdmin.query.filter(
GroupAdmin.admin_type == 'Group', GroupAdmin.admin_id.in_(q3)
).with_entities(GroupAdmin.group_id)
q5 = Membership.query.filter(
Membership.state == MembershipState.PENDING_ADMIN,
Membership.id_group.in_(q4))
query = q2.union(q5)
return query
|
Get a group s members.
|
def query_by_group(cls, group_or_id, with_invitations=False, **kwargs):
"""Get a group's members."""
if isinstance(group_or_id, Group):
id_group = group_or_id.id
else:
id_group = group_or_id
if not with_invitations:
return cls._filter(
cls.query.filter_by(id_group=id_group),
**kwargs
)
else:
return cls.query.filter(
Membership.id_group == id_group,
db.or_(
Membership.state == MembershipState.PENDING_USER,
Membership.state == MembershipState.ACTIVE
)
)
|
Modify query as so include only specific members.
|
def search(cls, query, q):
"""Modify query as so include only specific members.
:param query: Query object.
:param str q: Search string.
:returs: Query object.
"""
query = query.join(User).filter(
User.email.like('%{0}%'.format(q)),
)
return query
|
Modify query as so to order the results.
|
def order(cls, query, field, s):
"""Modify query as so to order the results.
:param query: Query object.
:param str s: Orderinig: ``asc`` or ``desc``.
:returs: Query object.
"""
if s == 'asc':
query = query.order_by(asc(field))
elif s == 'desc':
query = query.order_by(desc(field))
return query
|
Create a new membership.
|
def create(cls, group, user, state=MembershipState.ACTIVE):
"""Create a new membership."""
with db.session.begin_nested():
membership = cls(
user_id=user.get_id(),
id_group=group.id,
state=state,
)
db.session.add(membership)
return membership
|
Delete membership.
|
def delete(cls, group, user):
"""Delete membership."""
with db.session.begin_nested():
cls.query.filter_by(group=group, user_id=user.get_id()).delete()
|
Activate membership.
|
def accept(self):
"""Activate membership."""
with db.session.begin_nested():
self.state = MembershipState.ACTIVE
db.session.merge(self)
|
Create a new group admin.
|
def create(cls, group, admin):
"""Create a new group admin.
:param group: Group object.
:param admin: Admin object.
:returns: Newly created GroupAdmin object.
:raises: IntegrityError
"""
with db.session.begin_nested():
obj = cls(
group=group,
admin=admin,
)
db.session.add(obj)
return obj
|
Get specific GroupAdmin object.
|
def get(cls, group, admin):
"""Get specific GroupAdmin object."""
try:
ga = cls.query.filter_by(
group=group, admin_id=admin.get_id(),
admin_type=resolve_admin_type(admin)).one()
return ga
except Exception:
return None
|
Delete admin from group.
|
def delete(cls, group, admin):
"""Delete admin from group.
:param group: Group object.
:param admin: Admin object.
"""
with db.session.begin_nested():
obj = cls.query.filter(
cls.admin == admin, cls.group == group).one()
db.session.delete(obj)
|
Get all groups for for a specific admin.
|
def query_by_admin(cls, admin):
"""Get all groups for for a specific admin."""
return cls.query.filter_by(
admin_type=resolve_admin_type(admin), admin_id=admin.get_id())
|
Get count of admins per group.
|
def query_admins_by_group_ids(cls, groups_ids=None):
"""Get count of admins per group."""
assert groups_ids is None or isinstance(groups_ids, list)
query = db.session.query(
Group.id, func.count(GroupAdmin.id)
).join(
GroupAdmin
).group_by(
Group.id
)
if groups_ids:
query = query.filter(Group.id.in_(groups_ids))
return query
|
Get all social newtworks profiles
|
def all(self):
'''
Get all social newtworks profiles
'''
response = self.api.get(url=PATHS['GET_PROFILES'])
for raw_profile in response:
self.append(Profile(self.api, raw_profile))
return self
|
Based on some criteria filter the profiles and return a new Profiles Manager containing only the chosen items
|
def filter(self, **kwargs):
'''
Based on some criteria, filter the profiles and return a new Profiles
Manager containing only the chosen items
If the manager doen't have any items, get all the profiles from Buffer
'''
if not len(self):
self.all()
new_list = filter(lambda item: [True for arg in kwargs if item[arg] == kwargs[arg]] != [], self)
return Profiles(self.api, new_list)
|
we want to display the errors introduced by pixelation so we plot: * zero noise cg image fit * SNR 20 cg image fit * CRB for both
|
def dorun(SNR=20, sweeps=20, burn=8, noise_samples=10):
"""
we want to display the errors introduced by pixelation so we plot:
* zero noise, cg image, fit
* SNR 20, cg image, fit
* CRB for both
a = dorun(noise_samples=30, sweeps=24, burn=12, SNR=20)
"""
radii = np.linspace(2,10,8, endpoint=False)
crbs, vals, errs = [], [], []
for radius in radii:
print 'radius', radius
s,im = pxint(radius=radius, factor=4)
goodstate = s.state.copy()
common.set_image(s, im, 1.0/SNR)
tcrb = crb(s)
tval, terr = sample(s, im, 1.0/SNR, N=noise_samples, sweeps=sweeps, burn=burn)
crbs.append(tcrb)
vals.append(tval)
errs.append(terr)
return np.array(crbs), np.array(vals), np.array(errs), radii
|
returns the kurtosis parameter for direction d d = 0 is rho d = 1 is z
|
def _skew(self, x, z, d=0):
""" returns the kurtosis parameter for direction d, d=0 is rho, d=1 is z """
# get the top bound determined by the kurtosis
kval = (np.tanh(self._poly(z, self._kurtosis_coeffs(d)))+1)/12.
bdpoly = np.array([
-1.142468e+04, 3.0939485e+03, -2.0283568e+02,
-2.1047846e+01, 3.79808487e+00, 1.19679781e-02
])
top = np.polyval(bdpoly, kval)
# limit the skewval to be 0 -> top val
skew = self._poly(z, self._skew_coeffs(d))
skewval = top*(np.tanh(skew) + 1) - top
return skewval*(3*x - x**3)
|
returns the kurtosis parameter for direction d d = 0 is rho d = 1 is z
|
def _kurtosis(self, x, z, d=0):
""" returns the kurtosis parameter for direction d, d=0 is rho, d=1 is z """
val = self._poly(z, self._kurtosis_coeffs(d))
return (np.tanh(val)+1)/12.*(3 - 6*x**2 + x**4)
|
axis is z or xy seps = np. linspace ( 0 2 20 ) z seps = np. linspace ( - 2 2 20 ) xy
|
def fit_edge(separation, radius=5.0, samples=100, imsize=64, sigma=0.05, axis='z'):
"""
axis is 'z' or 'xy'
seps = np.linspace(0,2,20) 'z'
seps = np.linspace(-2,2,20) 'xy'
"""
terrors = []
berrors = []
crbs = []
for sep in separation:
print '='*79
print 'sep =', sep,
s = init.create_two_particle_state(imsize, radius=radius, delta=sep, sigma=0.05,
axis='z', psfargs={'params': (2.0,1.0,4.0), 'error': 1e-8},
stateargs={'sigmapad': True, 'pad': const.PAD})
# move off of a pixel edge (cheating for trackpy)
d = np.array([0,0.5,0.5])
s.obj.pos -= d
s.reset()
# move the particles to the edge
bl = s.blocks_particle(0)
s.update(bl[0], np.array([s.pad+radius]))
bl = s.blocks_particle(1)
s.update(bl[0], np.array([s.pad-radius]))
if axis == 'z':
bl = s.blocks_particle(1)
s.update(bl[0], s.state[bl[0]]-sep)
s.model_to_true_image()
if axis == 'xy':
bl = s.blocks_particle(1)
s.update(bl[2], s.state[bl[2]]+sep)
s.model_to_true_image()
# save where the particles were originally so we can jiggle
p = s.state[s.b_pos].reshape(-1,3).copy()
print p[0], p[1]
# calculate the CRB for this configuration
bl = s.explode(s.b_pos)
crbs.append(np.sqrt(np.diag(np.linalg.inv(s.fisher_information(blocks=bl)))).reshape(-1,3))
# calculate the featuring errors
tmp_tp, tmp_bf = [],[]
for i in xrange(samples):
print i
bench.jiggle_particles(s, pos=p, sig=0.3, mask=np.array([1,1,1]))
t = bench.trackpy(s)
b = bench.bamfpy_positions(s, sweeps=15)
tmp_tp.append(bench.error(s, t))
tmp_bf.append(bench.error(s, b))
terrors.append(tmp_tp)
berrors.append(tmp_bf)
return np.array(crbs), np.array(terrors), np.array(berrors)
|
scan jitter is in terms of the fractional pixel difference when moving the laser in the z - direction
|
def zjitter(jitter=0.0, radius=5):
"""
scan jitter is in terms of the fractional pixel difference when
moving the laser in the z-direction
"""
psfsize = np.array([2.0, 1.0, 3.0])
# create a base image of one particle
s0 = init.create_single_particle_state(imsize=4*radius,
radius=radius, psfargs={'params': psfsize, 'error': 1e-6})
sl = np.s_[s0.pad:-s0.pad,s0.pad:-s0.pad,s0.pad:-s0.pad]
# add up a bunch of trajectories
finalimage = 0*s0.get_model_image()[sl]
position = 0*s0.obj.pos[0]
for i in xrange(finalimage.shape[0]):
offset = jitter*np.random.randn(3)*np.array([1,0,0])
s0.obj.pos[0] = np.array(s0.image.shape)/2 + offset
s0.reset()
finalimage[i] = s0.get_model_image()[sl][i]
position += s0.obj.pos[0]
position /= float(finalimage.shape[0])
# place that into a new image at the expected parameters
s = init.create_single_particle_state(imsize=4*radius, sigma=0.05,
radius=radius, psfargs={'params': psfsize, 'error': 1e-6})
s.reset()
# measure the true inferred parameters
return s, finalimage, position
|
we want to display the errors introduced by pixelation so we plot: * CRB sampled error vs exposure time
|
def dorun(SNR=20, njitters=20, samples=10, noise_samples=10, sweeps=20, burn=10):
"""
we want to display the errors introduced by pixelation so we plot:
* CRB, sampled error vs exposure time
a = dorun(ntimes=10, samples=5, noise_samples=5, sweeps=20, burn=8)
"""
jitters = np.logspace(-6, np.log10(0.5), njitters)
crbs, vals, errs, poss = [], [], [], []
for i,t in enumerate(jitters):
print '###### jitter', i, t
for j in xrange(samples):
print 'image', j, '|',
s,im,pos = zjitter(jitter=t)
# typical image
common.set_image(s, im, 1.0/SNR)
crbs.append(crb(s))
val, err = sample(s, im, 1.0/SNR, N=noise_samples, sweeps=sweeps, burn=burn)
poss.append(pos)
vals.append(val)
errs.append(err)
shape0 = (njitters, samples, -1)
shape1 = (njitters, samples, noise_samples, -1)
crbs = np.array(crbs).reshape(shape0)
vals = np.array(vals).reshape(shape1)
errs = np.array(errs).reshape(shape1)
poss = np.array(poss).reshape(shape0)
return [crbs, vals, errs, poss, jitters]
|
Returns the detailed information on individual interactions with the social media update such as favorites retweets and likes.
|
def interactions(self):
'''
Returns the detailed information on individual interactions with the social
media update such as favorites, retweets and likes.
'''
interactions = []
url = PATHS['GET_INTERACTIONS'] % self.id
response = self.api.get(url=url)
for interaction in response['interactions']:
interactions.append(ResponseObject(interaction))
self.__interactions = interactions
return self.__interactions
|
Edit an existing individual status update.
|
def edit(self, text, media=None, utc=None, now=None):
'''
Edit an existing, individual status update.
'''
url = PATHS['EDIT'] % self.id
post_data = "text=%s&" % text
if now:
post_data += "now=%s&" % now
if utc:
post_data += "utc=%s&" % utc
if media:
media_format = "media[%s]=%s&"
for media_type, media_item in media.iteritems():
post_data += media_format % (media_type, media_item)
response = self.api.post(url=url, data=post_data)
return Update(api=self.api, raw_response=response['update'])
|
Immediately shares a single pending update and recalculates times for updates remaining in the queue.
|
def publish(self):
'''
Immediately shares a single pending update and recalculates times for
updates remaining in the queue.
'''
url = PATHS['PUBLISH'] % self.id
return self.api.post(url=url)
|
Permanently delete an existing status update.
|
def delete(self):
'''
Permanently delete an existing status update.
'''
url = PATHS['DELETE'] % self.id
return self.api.post(url=url)
|
Move an existing status update to the top of the queue and recalculate times for all updates in the queue. Returns the update with its new posting time.
|
def move_to_top(self):
'''
Move an existing status update to the top of the queue and recalculate
times for all updates in the queue. Returns the update with its new
posting time.
'''
url = PATHS['MOVE_TO_TOP'] % self.id
response = self.api.post(url=url)
return Update(api=self.api, raw_response=response)
|
Remove the noise poles from a 2d noise distribution to show that affects the real - space noise picture. noise -- fftshifted 2d array of q values
|
def pole_removal(noise, poles=None, sig=3):
"""
Remove the noise poles from a 2d noise distribution to show that affects
the real-space noise picture.
noise -- fftshifted 2d array of q values
poles -- N,2 list of pole locations. the last index is in the order y,x as
determined by mpl interactive plots
for example: poles = np.array([[190,277], [227,253], [233, 256]]
"""
center = np.array(noise.shape)/2
v = np.rollaxis(
np.array(
np.meshgrid(*(np.arange(s) for s in noise.shape), indexing='ij')
), 0, 3
).astype("float")
filter = np.zeros_like(noise, dtype='float')
for p in poles:
for pp in [p, center - (p-center)]:
dist = ((v-pp)**2).sum(axis=-1)
filter += np.exp(-dist / (2*sig**2))
filter[filter > 1] = 1
return noise*(1-filter)
|
Returns an array of updates that are currently in the buffer for an individual social media profile.
|
def pending(self):
'''
Returns an array of updates that are currently in the buffer for an
individual social media profile.
'''
pending_updates = []
url = PATHS['GET_PENDING'] % self.profile_id
response = self.api.get(url=url)
for update in response['updates']:
pending_updates.append(Update(api=self.api, raw_response=update))
self.__pending = pending_updates
return self.__pending
|
Returns an array of updates that have been sent from the buffer for an individual social media profile.
|
def sent(self):
'''
Returns an array of updates that have been sent from the buffer for an
individual social media profile.
'''
sent_updates = []
url = PATHS['GET_SENT'] % self.profile_id
response = self.api.get(url=url)
for update in response['updates']:
sent_updates.append(Update(api=self.api, raw_response=update))
self.__sent = sent_updates
return self.__sent
|
Randomize the order at which statuses for the specified social media profile will be sent out of the buffer.
|
def shuffle(self, count=None, utc=None):
'''
Randomize the order at which statuses for the specified social media
profile will be sent out of the buffer.
'''
url = PATHS['SHUFFLE'] % self.profile_id
post_data = ''
if count:
post_data += 'count=%s&' % count
if utc:
post_data += 'utc=%s' % utc
return self.api.post(url=url, data=post_data)
|
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