import os
import re
import copy
import json
import numpy as np
import cPickle as pickle
from functools import partial
from contextlib import contextmanager
from peri import util, comp, models
from peri.logger import log as baselog
log = baselog.getChild('states')
class UpdateError(Exception):
pass
def sample(field, inds=None, slicer=None, flat=True):
"""
Take a sample from a field given flat indices or a shaped slice
Parameters
-----------
inds : list of indices
One dimensional (raveled) indices to return from the field
slicer : slice object
A shaped (3D) slicer that returns a section of image
import re
from peri.comp import (
ComponentCollection, GlobalScalar, ilms, psfs, objs, exactpsf
)
from peri.logger import log as baselog
log = baselog.getChild('models')
allfields = {
'const': GlobalScalar,
'poly3d': ilms.Polynomial3D,
'leg3d': ilms.LegendrePoly3D,
'poly2p1d': ilms.Polynomial2P1D,
'leg2p1d': ilms.LegendrePoly2P1D,
'cheb2p1d': ilms.ChebyshevPoly2P1D,
'barnesleg2p1d': ilms.BarnesStreakLegPoly2P1D,
'combo': ComponentCollection,
}
allpsfs = {
'identity': psfs.IdentityPSF,
'gauss2d': psfs.AnisotropicGaussian,
'gauss3d': psfs.AnisotropicGaussianXYZ,
'gauss4d': psfs.Gaussian4DPoly,
'gauss4d-leg': psfs.Gaussian4DLegPoly,
'gauss4d-mom': psfs.GaussianMomentExpansion,
'linescan': exactpsf.ExactLineScanConfocalPSF,
'cheb-linescan': exactpsf.ChebyshevLineScanConfocalPSF,
'cheb-linescan-fixedss': exactpsf.FixedSSChebLinePSF,
}
arguments::
from peri.fft import fft, fftkwargs
fft.fftn(image_array, **fftkwargs)
"""
import atexit
import pickle
import numpy as np
from multiprocessing import cpu_count
from peri import conf
from peri.util import Tile
from peri.logger import log
log = log.getChild('fft')
try:
import pyfftw
hasfftw = True
except ImportError as e:
log.warning(
'FFTW not found, which can improve speed by 20x. '
'Try `pip install pyfftw`.'
)
hasfftw = False
FFTW_PLAN_FAST = 'FFTW_ESTIMATE'
FFTW_PLAN_NORMAL = 'FFTW_MEASURE'
FFTW_PLAN_SLOW = 'FFTW_PATIENT'
from __future__ import print_function
import os
import sys
import time
import inspect
import itertools
import numpy as np
from contextlib import contextmanager
from peri import initializers
from peri.logger import log
log = log.getChild('util')
#=============================================================================
# Tiling utilities
#=============================================================================
def oddify(num):
"""
Return the next odd number if ``num`` is even.
Examples
--------
>>> oddify(1)
1
>>> oddify(4)
5
"""
return num + (num % 2 == 0)
from builtins import range, zip
import numpy as np
import scipy.ndimage as nd
import peri
from peri import initializers
from peri.util import Tile
import peri.opt.optimize as opt
from peri.logger import log
CLOG = log.getChild('addsub')
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
from builtins import str, range
import os
import sys
import tempfile
import pickle
import numpy as np
from peri import states, util
from peri.mc import samplers, engines, observers
from peri.logger import log
log = log.getChild("mc.sample")
#=============================================================================
# Sampling methods that run through blocks and sample
#=============================================================================
def sample_state(state,
blocks,
stepout=1,
slicing=True,
N=1,
doprint=False,
procedure='uniform'):
eng = engines.SequentialBlockEngine(state)
opsay = observers.Printer()
ohist = observers.HistogramObserver(block=blocks)
eng.add_samplers([
from builtins import range
import glob
import itertools
from PIL import Image
import numpy as np
import scipy.ndimage as nd
from peri.logger import log
log = log.getChild("initializers")
#=======================================================================
# Image loading functions
#=======================================================================
def _sliceiter(img):
i = 0
while True:
try:
img.seek(i)
yield np.array(img)
i += 1
except EOFError as e:
break
def load_tiff(filename):
img = Image.open(filename)
return np.array(list(_sliceiter(img)))
from builtins import range, object
import numpy as np
import matplotlib as mpl
import matplotlib.pylab as pl
from matplotlib.gridspec import GridSpec
import peri.opt.optimize as opt
from peri.util import Tile
from peri.logger import log
log = log.getChild('interaction')
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`