sub2index and index2sub with calls to np.ravel_multi_index and np.unravel_index, respectively.
master
Per.Andreas.Brodtkorb 10 years ago
parent b992e8c979
commit c93efca266

@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<projectDescription> <projectDescription>
<name>pywafo</name> <name>svn_pywafo</name>
<comment></comment> <comment></comment>
<projects> <projects>
</projects> </projects>
@ -10,16 +10,6 @@
<arguments> <arguments>
</arguments> </arguments>
</buildCommand> </buildCommand>
<buildCommand>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>auto,full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/wafo_stats_tests.launch</value>
</dictionary>
</arguments>
</buildCommand>
</buildSpec> </buildSpec>
<natures> <natures>
<nature>org.python.pydev.pythonNature</nature> <nature>org.python.pydev.pythonNature</nature>

@ -1,10 +1,5 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?eclipse-pydev version="1.0"?> <?eclipse-pydev version="1.0"?><pydev_project>
<pydev_project>
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
<path>/pywafo/src</path>
</pydev_pathproperty>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property> <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property> <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
</pydev_project> </pydev_project>

@ -1,60 +0,0 @@
"""
builds all extensions
In notepad (or your favourite text editor) create a new text file and enter the following in the file:
[build]
compiler = mingw32
Save the file as "C:\Python25\Lib\distutils\distutils.cfg".
This will tell python to use the MinGW compiler when compiling extensions
See also http://www.scipy.org/Cookbook/CompilingExtensionsOnWindowsWithMinGW
"""
import os
import shutil
def compile_all():
wd = os.getcwd()
pkg_name = 'wafo'
root_dir = os.path.join(wd,'src',pkg_name)
root_src = os.path.join(root_dir, 'source')
buildscript = 'build_all.py'
# if Linux
if os.name == 'posix':
build_call = 'python %s' % buildscript
lib_ext = '.so'
# On Windows
elif os.name == 'nt':
build_call = 'python.exe %s' % buildscript
lib_ext = '.pyd'
# give an Error for other OS-es
else:
raise UserWarning, \
'Untested platform:', os.name
for root, dirs, files in os.walk(root_src):
dir1 = [dir for dir in dirs if not os.path.exists(os.path.join(root,dir,buildscript))]
for dir in dir1:
dirs.remove(dir) ## don't visit directories without buildscript
if buildscript in files:
print('Building: ', root)
#buildfile ='python.exe %s' % os.path.join(root,buildscript)
os.chdir(root)
t = os.system(build_call)
print(t)
for file in os.listdir('.'):
if file.endswith(lib_ext):
dest_file = os.path.join(root_dir, file)
if os.path.exists(dest_file):
os.remove(dest_file)
shutil.copy(os.path.join(root,file), root_dir)
os.chdir(wd)
if __name__=='__main__':
compile_all()

@ -16,38 +16,35 @@ python setup.py sdist bdist_wininst upload --show-response
#!/usr/bin/env python #!/usr/bin/env python
import os import os
import shutil
import sys import sys
import subprocess import subprocess
import re import re
import warnings import warnings
from Cython.Build import cythonize
MAJOR = 0 MAJOR = 0
MINOR = 1 MINOR = 1
MICRO = 2 MICRO = 2
ISRELEASED = False ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO) VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
# sys.argv.append("build_src")
# sys.argv.append("build_ext")
# sys.argv.append("--inplace")
# sys.argv.append("develop") # sys.argv.append("develop")
# sys.argv.append("install") # sys.argv.append("install")
DISTUTILS_DEBUG = True DISTUTILS_DEBUG = True
pkg_name = 'wafo' PKG_NAME = 'wafo'
root_dir = os.path.join('src',pkg_name) ROOT_DIR = os.path.join('src',PKG_NAME)
# make sure we import from this package, not an installed one: # make sure we import from this package, not an installed one:
sys.path.insert(0, root_dir) sys.path.insert(0, ROOT_DIR)
import info import info
#import wafo
if True: #__file__ == 'setupegg.py': from setuptools import find_packages # setup, Extension
# http://peak.telecommunity.com/DevCenter/setuptools from numpy.distutils.core import setup, Extension # as FExtension
from setuptools import setup, Extension, find_packages
else:
from distutils.core import setup
# Return the svn version as a string, raise a ValueError otherwise
def svn_version(): def svn_version():
'''Return the svn version as a string, raise a ValueError otherwise'''
from numpy.compat import asstr from numpy.compat import asstr
env = os.environ.copy() env = os.environ.copy()
@ -84,58 +81,106 @@ short_version='%(version)s'
version='%(version)s' version='%(version)s'
release=%(isrelease)s release=%(isrelease)s
""" """
fid = open(os.path.join(root_dir,filename), 'w') fid = open(os.path.join(ROOT_DIR,filename), 'w')
try: try:
fid.write(cnt % {'version': VERSION, 'isrelease': str(ISRELEASED)}) fid.write(cnt % {'version': VERSION, 'isrelease': str(ISRELEASED)})
finally: finally:
fid.close() fid.close()
if __name__=='__main__':
write_version_py()
def get_library_extension():
'''Return extension of an executable library'''
if os.name == 'posix': # executable library on Linux has extension .so
lib_ext = '.so'
elif os.name == 'nt': # extension on Windows is .pyd
lib_ext = '.pyd'
else:
raise UserWarning('Platform not supported:', os.name)
return lib_ext
def compile_all():
wd = os.getcwd()
root_dir = os.path.join(wd,'src',PKG_NAME)
root_src = os.path.join(root_dir, 'source')
buildscript = 'build_all.py'
lib_ext = get_library_extension()
if os.name == 'nt': # On Windows
build_call = 'python.exe %s' % buildscript
else:
build_call = 'python %s' % buildscript
for root, dirs, files in os.walk(root_src):
dir1 = [dir for dir in dirs
if not os.path.exists(os.path.join(root, dir, buildscript))]
for dir in dir1:
dirs.remove(dir) # don't visit directories without buildscript
if buildscript in files:
print('Building: ', root)
os.chdir(root)
t = os.system(build_call)
print(t)
for file in os.listdir('.'):
if file.endswith(lib_ext):
dest_file = os.path.join(root_dir, file)
if os.path.exists(dest_file):
os.remove(dest_file)
shutil.copy(os.path.join(root, file), root_dir)
os.chdir(wd)
def setup_package():
write_version_py()
join = os.path.join
packages = find_packages('src') packages = find_packages('src')
for p in packages: for p in packages:
print(p) print(p)
package_paths =[p.replace(pkg_name+'.','').replace(pkg_name,'').replace('.',os.path.sep) for p in packages] def convert_package2path(p):
test_paths = [os.path.join(pkg_path,'test') for pkg_path in package_paths return p.replace(PKG_NAME + '.',
if os.path.exists(os.path.join(root_dir,pkg_path,'test'))] '').replace(PKG_NAME, '').replace('.', os.path.sep)
testscripts = [os.path.join(subtst, f) for subtst in test_paths package_paths = [convert_package2path(p) for p in packages]
for f in os.listdir(os.path.join(root_dir, subtst)) test_paths = [join(pkg_path, 'test') for pkg_path in package_paths
if os.path.exists(join(ROOT_DIR, pkg_path, 'test'))]
testscripts = [join(subtst, f) for subtst in test_paths
for f in os.listdir(join(ROOT_DIR, subtst))
if not (f.startswith('.') or f.endswith('~') or if not (f.startswith('.') or f.endswith('~') or
f.endswith('.old') or f.endswith('.bak'))] f.endswith('.old') or f.endswith('.bak'))]
#subpackages = ('spectrum','data','transform','covariance')
#subpackagesfull = [os.path.join(pkg_name,f) for f in subpackages]
#subtests = [os.path.join(subpkg,'test') for subpkg in subpackages]
#testscripts = [os.path.join(subtst, f) for subtst in subtests
# for f in os.listdir(os.path.join(root_dir, subtst))
# if not (f.startswith('.') or f.endswith('~') or
# f.endswith('.old') or f.endswith('.bak'))]
datadir = 'data' datadir = 'data'
datafiles = [os.path.join(datadir, f) for f in os.listdir(os.path.join(root_dir, datadir)) datafiles = [join(datadir, f) for f in os.listdir(join(ROOT_DIR, datadir))
if not (f.startswith('.') or f.endswith('~') or if not (f.startswith('.') or f.endswith('~') or
f.endswith('.old') or f.endswith('.bak') or f.endswith('.old') or f.endswith('.bak') or
f.endswith('.py') or f.endswith('test') )] f.endswith('.py') or f.endswith('test') )]
if 'build_ext' in sys.argv:
# executable library on Linux has extension .so compile_all()
if os.name == 'posix': lib_ext = get_library_extension()
lib_ext = '.so' libs = [f for f in os.listdir(join(ROOT_DIR)) if f.endswith(lib_ext)]
# extension on Windows is .pyd packagedata = testscripts + datafiles + libs
elif os.name == 'nt':
lib_ext = '.pyd' # ext_module_list = cythonize(join(ROOT_DIR, "primes.pyx"))
#
# give an Error for other OS-es # for ext_module in ext_module_list:
else: # if not isinstance(ext_module, Extension):
raise UserWarning, \ # ext_module.__class__ = Extension
'Platform not supported:', os.name
# for name, src_files in [('mvn',('mvn.pyf', 'mvndst.f')),
libs = [f for f in os.listdir(os.path.join(root_dir)) if f.endswith(lib_ext) ] # ('c_library',('c_library.pyf', 'c_functions.c'))]:
# libs = [f for f in os.listdir(os.path.join(root_dir)) if f.endswith('.pyd') ] # sources = [join(ROOT_DIR, 'source', name, f) for f in src_files]
# ext_module_list.append(Extension(name='%s.%s' % (PKG_NAME, name),
packagedata = testscripts + datafiles + libs #['c_library.pyd'] #,'disufq1.c','diffsumfunq.pyd','diffsumfunq.pyf','findrfc.c','rfc.pyd','rfc.pyf'] # sources=sources))
# sources = [join(ROOT_DIR, 'source', 'mreg', 'cov2mmpdfreg_intfc.f'), ]
# libs = [join(ROOT_DIR, 'source', 'mreg', f)
# for f in ['dsvdc', 'mregmodule', 'intfcmod'] ]
# ext_module_list.append(Extension(name='wafo.covmod', sources=sources,
# libraries=libs))
# mvn_sources = [join(root_mvn, 'source', 'mvn', 'mvn.pyf'),
# join(root_mvn, 'source', 'mvn','mvndst.f')]
# ext_module_list.append(Extension(name='wafo.mvn', sources=mvn_sources))
setup( setup(
version = VERSION, version = VERSION,
@ -146,10 +191,11 @@ if __name__=='__main__':
install_requires = ['numpy>=1.4','numdifftools>=0.2'], install_requires = ['numpy>=1.4','numdifftools>=0.2'],
license = "GPL", license = "GPL",
url='http://code.google.com/p/pywafo/', url='http://code.google.com/p/pywafo/',
name = pkg_name, name = PKG_NAME,
package_dir = {'': 'src'}, package_dir = {'': 'src'},
packages = packages, packages = packages,
package_data = {'': packagedata}, package_data = {'': packagedata},
# ext_modules = ext_module_list,
classifiers=[ classifiers=[
'Development Status :: 4 - Beta', 'Development Status :: 4 - Beta',
'Intended Audience :: Education', 'Intended Audience :: Education',
@ -159,11 +205,8 @@ if __name__=='__main__':
'Programming Language :: Python :: 2.6', 'Programming Language :: Python :: 2.6',
'Topic :: Scientific/Engineering :: Mathematics', 'Topic :: Scientific/Engineering :: Mathematics',
], ],
#packages = [package_name,] + list(subpackagesfull),
#package_data = {package_name: packagedata},
#package_data = {'': ['wafo.cfg']},
#scripts = [os.path.join('bin', f)
# for f in os.listdir('bin')
# if not (f.startswith('.') or f.endswith('~') or
# f.endswith('.old') or f.endswith('.bak'))],
) )
if __name__=='__main__':
setup_package()

@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
""" """
f2py c_library.pyf c_functions.c -c f2py c_library.pyf c_functions.c -c
@ -61,3 +62,4 @@ def f2py_call_str():
except NameError: except NameError:
raise UserWarning('Couldn\'t locate f2py. ' raise UserWarning('Couldn\'t locate f2py. '
'Should be part of NumPy installation.') 'Should be part of NumPy installation.')

@ -8,6 +8,7 @@ from scipy import special as sp
from wafo.plotbackend import plotbackend as plt from wafo.plotbackend import plotbackend as plt
from scipy.integrate import simps, trapz from scipy.integrate import simps, trapz
from wafo.demos import humps from wafo.demos import humps
from pychebfun import Chebfun
_EPS = np.finfo(float).eps _EPS = np.finfo(float).eps
_POINTS_AND_WEIGHTS = {} _POINTS_AND_WEIGHTS = {}
@ -1423,8 +1424,208 @@ def test_docstrings():
doctest.testmod() doctest.testmod()
def levin_integrate():
''' An oscillatory integral
Sheehan Olver, December 2010
(Chebfun example quad/LevinIntegrate.m)
This example computes the highly oscillatory integral of
f * exp( 1i * w * g ),
over (0,1) using the Levin method [1]. This method computes the integral
by rewriting it as an ODE
u' + 1i * w * g' u = f,
so that the indefinite integral of f * exp( 1i * w * g ) is
u * exp( 1i * w * g ).
We use as an example
f = 1 / ( x + 2 );
g = cos( x - 2 );
w = 100000;
#
References:
[1] Levin, D., Procedures for computing one and two-dimensional integrals
of functions with rapid irregular oscillations, Maths Comp., 38 (1982) 531--538
'''
exp = np.exp
domain=[0, 1]
x = Chebfun.identity(domain=domain)
f = 1./(x+2)
g = np.cos(x-2)
D = np.diff(domain)
# Here is are plots of this integrand, with w = 100, in complex space
w = 100;
line_opts = dict(line_width=1.6)
font_opts = dict(font_size= 14)
#
intg = f*exp(1j*w*g)
xs, ys, xi, yi, d = intg.plot_data(1000)
#intg.plot(with_interpolation_points=True)
#xi = np.linspace(0, 1, 1024)
# plt.plot(xs, ys) # , **line_opts)
# plt.plot(xi, yi, 'r.')
# #axis equal
# plt.title('Complex plot of integrand') #,**font_opts)
# plt.show('hold')
##
# and of just the real part
# intgr = np.real(intg)
# xs, ys, xi, yi, d = intgr.plot_data(1000)
#intgr.plot()
# plt.plot(xs, np.real(ys)) # , **line_opts)
# plt.plot(xi, np.real(yi), 'r.')
#axis equal
# plt.title('Real part of integrand') #,**font_opts)
# plt.show('hold')
##
# The Levin method will be accurate for large and small w, and the time
# taken is independent of w. Here we take a reasonably large value of w.
w = 1000;
intg = f*exp(1j*w*g)
val0 = np.sum(intg)
# val1 = sum(intg)
print(val0)
##
# Start timing
#tic
##
# Construct the operator L
L = D + 1j*w*np.diag(g.differentiate())
##
# From asymptotic analysis, we know that there exists a solution to the
# equation which is non-oscillatory, though we do not know what initial
# condition it satisfies. Thus we find a particular solution to this
# equation with no boundary conditions.
u = L / f
##
# Because L is a differential operator with derivative order 1, \ expects
# it to be given a boundary condition, which is why the warning message is
# displayed. However, this doesn't cause any problems: though there are,
# in fact, a family of solutions to the ODE without boundary conditions
# due to the kernel
#
# exp(- 1i * w * g),
#
# it does not actually matter which particular solution is computed.
# Non-uniqueness is also not an issue: \ in matlab is least squares, hence
# does not require uniqueness. The existence of a non-oscillatory solution
# ensures that \ converges to a u with length independent of w.
#
# One could prevent the warning by applying a boundary condition consistent
# with the rest of the system, that is
# L.lbc = {L(1,:),f(0)};
##
# Now we evaluate the antiderivative at the endpoints to obtain the
# integral.
u(1)*exp(1j*w*g(1)) - u(0)*exp(1j*w*g(0))
#toc
##
# Here is a way to compute the integral using Clenshaw--Curtis quadrature.
# As w becomes large, this takes an increasingly long time as the
# oscillations must be resolved.
#tic
sum( f*exp(1j*w*g) )
#toc
# aLevinTQ[omega_,a_,b_,f_,g_,nu_,wprec_,prm_,test_,basis_,np_]:=
#
# Module[{r,betam,A,AA,BB,S,F,w=N[omega, wprec]},
# M=Length[nu]-1;
# PB[k_,t_]:=If[basis==1,t^k,ChebyshevT[k,t]];
#
# ff[t_]:=((b-a)/2)*f[(b-a)*t/2+(a+b)/2];
#
# gg[t_]:=g[(b-a)*t/2+(a+b)/2];
# dgg[t_]:=Derivative[1][gg][t];
#
# If[test==0, betam=Min[Abs[dgg[-1]*w], Abs[dgg[1]*w]];
# While[prm*M/betam >=1, betam=2*betam]];
# If[test>0,x[k_]:=N[Cos[k*Pi/M], wprec],x[k_]:=
# Which[k<prm*M, N[-1+k/betam, wprec], k==Ceiling[prm*M],0,
# k>prm*M, N[1-(M-k)/betam, wprec]]];
#
# Psi[k_,t_]:=Derivative[0,1][PB][k,t]+I*w*dgg[t]*PB[k,t];
#
# ne[j_]:=nu[[j+1]]; S[-1]=0; S[j_]:=Sum[ne[i],{i,0,j}];
# nn=S[M]-1;
# A=ConstantArray[0,{nn+1,nn+1}];
# F=ConstantArray[0,nn+1]; r=0;
# While[r<M+1, Do[Do[ AA[j,k]=
# Limit[Derivative[0,Mod[j-S[r-1],ne[r]]][Psi][k,t],t->x[r]],
# {k,0,S[M]-1}],{j,S[r-1],S[r]-1}];
#
# Do[BB[j]=Limit[Derivative[Mod[j-S[r-1],ne[r]]][ff][t],
# t->x[r]],{j,S[r-1],S[r]-1}];
# Do[F[[j]]=BB[j-1],{j,S[r-1]+1,S[r]}];
# Do[Do[A[[j,k]]=AA[j-1,k-1],{k,1,S[M]}],{j,S[r-1]+1,S[r]}];
# r=r+1;]; (*sv=SingularValueList[N[A,wprec]];
# con=sv[[1]]/sv[[-1]]; Print["cond2(A)= ",N[con,3]];*)
# LS=Block[{MaxExtraPrecision=0},LeastSquares[N[A, wprec],F]];
# vvv[t_]:=Sum[LS[[k+1]]*PB[k,t], {k,0,nn}];
# NR=vvv[1]*Exp[I*w*gg[1]]-vvv[-1]*Exp[I*w*gg[-1]];
# Print["n=", np+ii+2s-2, ", Result= ", N[NR, wprec/2+5]];
# If[ii==0,PR=NR];];
# (* End of subroutine aLevinTQ /A.I. Hascelik, July 2013/ *)
#
# def main_levin():
# a=1; b=2;
# omega=100;
# prm=1/2;
# f[t_]=Exp[4t]
# g[t_]=t+Exp[4t]*Gamma[t]
#
# dg[t_]:=Derivative[1][g][t];
#
# prec=16
# wprec=2*prec
# delta = min(abs(omega*dg(a)), abs(omega*dg(b)))
# alpha = min(abs(omega*g(a)), abs(omega*g(b)))
# s=1; #(*if s>1, the integral is computed by Q_s^L*)
# test= 1 if delta<10 or alpha <=10 or s>1 else 0
#
# m = 1 if s>1 else np.floor(prec/max(np.log10(beta+1),1)+2)
# nc = 2*m+1 #(*or np=2m, number of collocation points*)
# basis=1; # (*take basis=0 for the Chebysev basis*)
# for ii in range(0, 2, 2):
# nu = np.ones((nc+ii,)) # ConstantArray[1,nc+ii];
# nu[0] = s
# nu[-1] = s
# #nu[[1]]=s;
# #nu[[-1]]=s;
# aLevinTQ[omega,a,b,f,g,nu,wprec,prm,test,basis,nc],
# #{ii,0,2,2}];
# Print["Error= ",Abs[NR-PR]];
if __name__ == '__main__': if __name__ == '__main__':
test_docstrings() levin_integrate()
# test_docstrings()
# qdemo(np.exp, 0, 3, plot_error=True) # qdemo(np.exp, 0, 3, plot_error=True)
# plt.show('hold') # plt.show('hold')
# main() # main()

@ -240,29 +240,7 @@ def args_flat(*args):
raise ValueError('Number of arguments must be 1 or 3!') raise ValueError('Number of arguments must be 1 or 3!')
def _check_and_adjust_shape(shape, nsub=None): def index2sub(shape, index, order='C'):
s = np.atleast_1d(shape)
ndim = len(s)
if ndim < 1:
raise ValueError('Shape vector must have at least 1 element.')
ndim = len(s)
if nsub is None:
nsub = ndim
if ndim <= nsub: # add trailing singleton dimensions
s = np.hstack([s, np.ones(nsub - ndim, dtype=int)])
else: # Adjust for linear indexing on last element
s = np.hstack([s[:nsub - 1], np.prod(s[nsub - 1:])])
return s
def _sub2index_factor(shape, order='C'):
'''Return multiplier needed for calculating linear index from subscripts.
'''
step = 1 if order == 'F' else -1 # C order
return np.hstack([1, np.cumprod(shape[::step][:-1])])[::step]
def index2sub(shape, index, nsub=None, order='C'):
''' '''
Returns Multiple subscripts from linear index. Returns Multiple subscripts from linear index.
@ -272,8 +250,6 @@ def index2sub(shape, index, nsub=None, order='C'):
shape of array shape of array
index : index :
linear index into array linear index into array
nsub : int optional
Number of subscripts returned. default nsub=len(shape)
order : {'C','F'}, optional order : {'C','F'}, optional
The order of the linear index. The order of the linear index.
'C' means C (row-major) order. 'C' means C (row-major) order.
@ -300,18 +276,7 @@ def index2sub(shape, index, nsub=None, order='C'):
-------- --------
sub2index sub2index
''' '''
ndx = np.atleast_1d(index) return np.unravel_index(index, shape, order=order)
s = _check_and_adjust_shape(shape, nsub)
k = _sub2index_factor(s, order)
n = len(s)
step = -1 if order == 'F' else 1 # C order
subscripts = [0, ] * n
for i in range(n)[::step]:
vi = np.remainder(ndx, k[i])
subscript = np.array((ndx - vi) / k[i], dtype=int)
subscripts[i] = subscript
ndx = vi
return tuple(subscripts)
def sub2index(shape, *subscripts, **kwds): def sub2index(shape, *subscripts, **kwds):
@ -350,21 +315,7 @@ def sub2index(shape, *subscripts, **kwds):
-------- --------
index2sub index2sub
''' '''
nsub = len(subscripts) return np.ravel_multi_index(subscripts, shape, **kwds)
s = _check_and_adjust_shape(shape, nsub)
k = _sub2index_factor(s, **kwds)
ndx = 0
s0 = np.shape(subscripts[0])
for i, subscript in enumerate(subscripts):
np.testing.assert_equal(
s0, np.shape(subscript),
'The subscripts vectors must all be of the same shape.')
if (np.any(subscript < 0)) or (np.any(s[i] <= subscript)):
raise IndexError('Out of range subscript.')
ndx = ndx + k[i] * subscript
return ndx
def is_numlike(obj): def is_numlike(obj):

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