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Commit 2fe46b65 authored by jansen31's avatar jansen31
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code readability

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proxtoolbox/Algorithms/RAAR.py
View file @ 2fe46b65
......@@ -19,7 +19,7 @@ class RAAR(SimpleAlgorithm):
beta_max = self.config['beta_max']
beta_switch = self.config['beta_switch']
tmp1 = 2*self.prox2.work(u)-u
tmp2=self.prox1.work(tmp1)
tmp2 = self.prox1.work(tmp1)
# update
beta = exp((-iter/beta_switch)**3)*beta0+(1-exp((-iter/beta_switch)**3))*beta_max # unrelaxes as the
unew = (beta*(2*tmp2-tmp1) + (1-beta)*tmp1 + u)/2
......
proxtoolbox/Problems/OrbitalTomog/Coronene_demo.py
View file @ 2fe46b65
import sys
# sys.path.append('../proxtoolbox/Problems/Phase')
sys.path.append('..')
from . import coronene_test
from .phase import Phase
# sys.path.append('../proxtoolbox/Problems/Phase')
orbit = Phase(coronene_test.new_config)
......
proxtoolbox/Problems/OrbitalTomog/phase.py
View file @ 2fe46b65
......@@ -15,8 +15,7 @@ class Phase(Problem):
"""
Phase Problem
"""
config = {
}
config = { } # This line does not do anything.
def __init__(self, new_config={}):
"""
......
proxtoolbox/Problems/Phase/tasse_ap_in.py
View file @ 2fe46b65
## This is the input file that the user sees/modifies. It should be simple,
## avoid jargon or acronyms, and should be a model for a menu-driven GUI
# This is the input file that the user sees/modifies. It should be simple,
# avoid jargon or acronyms, and should be a model for a menu-driven GUI
new_config = {
## We start very general.
##==========================================
## Problem parameters
##==========================================
## What is the name of the data file?
'data_filename' : 'Goettingen_data_processor',
## What type of object are we working with?
## Options are: 'phase', 'real', 'nonnegative', 'complex'
'object' : 'nonnegative',
## What type of constraints do we have?
## Options are: 'support only', 'real and support', 'nonnegative and support',
## 'amplitude only', 'sparse real', 'sparse complex', and 'hybrid'
'constraint' : 'nonnegative and support',
## What type of measurements are we working with?
## Options are: 'single diffraction', 'diversity diffraction',
## 'ptychography', and 'complex'
'experiment' : 'CDI',
## Next we move to things that most of our users will know
## better than we will. Some of these may be overwritten in the
## data processor file which the user will most likely write.
## Are the measurements in the far field or near field?
## Options are: 'far field' or 'near field',
'distance' : 'far field',
## What are the dimensions of the measurements?
'Nx' : 128,
'Ny' : 128,
'fresnel_nr' : 0,
#moved this to phase
#if(strcmp('distance,'near field'))
# 'fresnel_nr' : 1*2*pi*'Nx,
#else
# 'fresnel_nr' : 0, #1*2*pi*'Nx,
'magn' : 1,
## What are the noise characteristics (Poisson or Gaussian)?
'noise' : 'Poisson',
##==========================================
## Algorithm parameters
##==========================================
## Now set some algorithm parameters that the user should be
## able to control (without too much damage)
## Algorithm:
'algorithm' : 'AP', # used to be 'Projection',
'numruns' : 1, # the only time this parameter will
# be different than 1 is when we are
# benchmarking...not something a normal user
# would be doing.
## The following are parameters specific to RAAR, HPR, and HAAR that the
## user should be able to set/modify. Surely
## there will be other algorithm specific parameters that a user might
## want to play with. Don't know how best
## to do this. Thinking of a GUI interface, we could hard code all the
## parameters the user might encounter and have the menu options change
## depending on the value of the 'method field.
## do different things depending on the chosen algorithm:
#if(strcmp('method,'RAAR')||strcmp('method,'AP')||...
# strcmp('method,'HPR')||strcmp('method,'HAAR'))
# We start very general.
# =========================================
# Problem parameters
# =========================================
# What is the name of the data file?
'data_filename': 'Goettingen_data_processor',
# What type of object are we working with?
# Options are: 'phase', 'real', 'nonnegative', 'complex'
'object': 'nonnegative',
# What type of constraints do we have?
# Options are: 'support only', 'real and support', 'nonnegative and support',
# 'amplitude only', 'sparse real', 'sparse complex', and 'hybrid'
'constraint': 'nonnegative and support',
# What type of measurements are we working with?
# Options are: 'single diffraction', 'diversity diffraction',
# 'ptychography', and 'complex'
'experiment': 'CDI',
# Next we move to things that most of our users will know
# better than we will. Some of these may be overwritten in the
# data processor file which the user will most likely write.
# Are the measurements in the far field or near field?
# Options are: 'far field' or 'near field',
'distance': 'far field',
# What are the dimensions of the measurements?
'Nx': 128,
'Ny': 128,
'fresnel_nr': 0,
# moved this to phase
# if(strcmp('distance,'near field'))
# 'fresnel_nr' : 1*2*pi*'Nx,
# else
# 'fresnel_nr' : 0, #1*2*pi*'Nx,
'magn': 1,
# What are the noise characteristics (Poisson or Gaussian)?
'noise': 'Poisson',
# ==========================================
# Algorithm parameters
# ==========================================
# Now set some algorithm parameters that the user should be
# able to control (without too much damage)
# Algorithm:
'algorithm': 'AP', # used to be 'Projection',
'numruns': 1, # the only time this parameter will
# be different than 1 is when we are
# benchmarking...not something a normal user
# would be doing.
# The following are parameters specific to RAAR, HPR, and HAAR that the
# user should be able to set/modify. Surely
# there will be other algorithm specific parameters that a user might
# want to play with. Don't know how best
# to do this. Thinking of a GUI interface, we could hard code all the
# parameters the user might encounter and have the menu options change
# depending on the value of the 'method field.
# do different things depending on the chosen algorithm:
# if(strcmp('method,'RAAR')||strcmp('method,'AP')||...
# strcmp('method,'HPR')||strcmp('method,'HAAR'))
# the following just points this driver to a patch that communicates
# the parameters defined at this level to the structures used in the
# algorithms developed by Russell.
'problem_family' : 'Phase',
#else # moreregularization parameters for Thorsten's algorithms:
# prbl' : complete_itreg_par(prbl),
'problem_family': 'Phase',
# else # moreregularization parameters for Thorsten's algorithms:
# prbl' : complete_itreg_par(prbl),
# This is just a patch to Thorsten's tools. May want to change this
# later
#'problem_family='Hohage',
#end
#if(strcmp('problem_family,'Phase'))
## maximum number of iterations and tolerances
'MAXIT' : 5000,
'TOL' : 1e-10,
## relaxaton parameters in RAAR, HPR and HAAR
'beta_0' : 0.85, #0.95 # starting relaxation prameter (only used with
# HAAR, HPR and RAAR)
'beta_max' :0.50, # maximum relaxation prameter (only used with
# HAAR, RAAR, and HPR)
'beta_switch' : 30, # iteration at which beta moves from beta_0 -> beta_max
## parameter for the data regularization
## need to discuss how/whether the user should
## put in information about the noise
'data_ball' : .999826,
# 'problem_family='Hohage',
# end
# if(strcmp('problem_family,'Phase'))
# maximum number of iterations and tolerances
'MAXIT': 5000,
'TOL': 1e-10,
# relaxaton parameters in RAAR, HPR and HAAR
'beta_0': 0.85, # 0.95 # starting relaxation parameter (only used with HAAR, HPR and RAAR)
'beta_max': 0.50, # maximum relaxation prameter (only used with HAAR, RAAR, and HPR)
'beta_switch': 30, # iteration at which beta moves from beta_0 -> beta_max
# parameter for the data regularization
# need to discuss how/whether the user should
# put in information about the noise
'data_ball': .999826,
# 'data_ball' : .9998261e-0,
# the above is the percentage of the gap
# between the measured data and the
......@@ -112,50 +106,49 @@ new_config = {
# Ultimately the size of the gap depends
# on the inconsistency of the measurement model
# with the qualitative constraints.
#elseif(strcmp('problem_family,'Hohage'))
# 'alpha0' : 1e4,
# 'N_CG' : 70,
#end
# ##==========================================
# ## parameters for plotting and diagnostics
# ##==========================================
# 'plotWhat.n1=2,
# 'plotWhat.n2=3,
# 'plotWhat.plots' : 'PYWpyw',
# 'verbose' : 1, # options are 0 or 1
# 'graphics' : 1, # whether or not to display figures, options are 0 or 1.
# # default is 1.
# 'anim' : 1, # whether or not to disaply ``real time" reconstructions
# # options are 0=no, 1=yes, 2=make a movie
# # default is 1.
# 'graphics_display' : [], # unless specified, a default
# # plotting subroutine will generate
# # the graphics. Otherwise, the user
# # can write their own plotting subroutine
#
##==========================================
## parameters for plotting and diagnostics
##==========================================
'diagnostic' : True,
'verbose' : 1, # options are 0 or 1
'graphics' : 1, # whether or not to display figures, options are 0 or 1.
# default is 1.
'anim' : 2, # whether or not to disaply ``real time" reconstructions
# options are 0=no, 1=yes, 2=make a movie
# default is 1.
'graphics_display' : 'Phase_graphics' # unless specified, a default
# plotting subroutine will generate
# the graphics. Otherwise, the user
# can write their own plotting subroutine
# elseif(strcmp('problem_family,'Hohage'))
# 'alpha0' : 1e4,
# 'N_CG' : 70,
# end
# ##==========================================
# ## parameters for plotting and diagnostics
# ##==========================================
# 'plotWhat.n1=2,
# 'plotWhat.n2=3,
# 'plotWhat.plots' : 'PYWpyw',
# 'verbose' : 1, # options are 0 or 1
# 'graphics' : 1, # whether or not to display figures, options are 0 or 1.
# # default is 1.
# 'anim' : 1, # whether or not to disaply ``real time" reconstructions
# # options are 0=no, 1=yes, 2=make a movie
# # default is 1.
# 'graphics_display' : [], # unless specified, a default
# # plotting subroutine will generate
# # the graphics. Otherwise, the user
# # can write their own plotting subroutine
#
# ==========================================
# parameters for plotting and diagnostics
# ==========================================
'diagnostic': True,
'verbose': 1, # options are 0 or 1
'graphics': 1, # whether or not to display figures, options are 0 or 1.
# default is 1.
'anim': 2, # whether or not to disaply ``real time" reconstructions
# options are 0=no, 1=yes, 2=make a movie
# default is 1.
'graphics_display': 'Phase_graphics' # unless specified, a default
# plotting subroutine will generate
# the graphics. Otherwise, the user
# can write their own plotting subroutine
}
##======================================================================
## Technical/software specific parameters
##======================================================================
## Given the parameter values above, the following technical/algorithmic
## parameters are automatically set. The user does not need to know
## about these details, and so probably these parameters should be set in
## a module one level below this one.
# =====================================================================
# Technical/software specific parameters
# =====================================================================
# Given the parameter values above, the following technical/algorithmic
# parameters are automatically set. The user does not need to know
# about these details, and so probably these parameters should be set in
# a module one level below this one.
proxtoolbox/Problems/problems.py
View file @ 2fe46b65
......@@ -7,14 +7,14 @@ Created on Wed Oct 15 11:36:27 2014
import time
__all__ = ["Problem"]
class Problem:
"""
Generic interface for ProxToolbox problems
"""
def __init__(self, config={}):
"""
Initialization method
......@@ -26,7 +26,7 @@ class Problem:
If unspecified, a default configuration will be used.
"""
raise NotImplementedError("This is just an abstract interface")
def _presolve(self):
"""
Preprocessing data.
......@@ -39,14 +39,14 @@ class Problem:
This procedure solves the problem.
"""
raise NotImplementedError("This is just an abstract interface")
def _postsolve(self):
"""
Postprocessing data.
This procedure is called after the problem has been solved.
"""
raise NotImplementedError("This is just an abstract interface")
def solve(self):
"""
Solves the problem, as specified by _presolve, _solve and _postsolve.
......@@ -54,14 +54,14 @@ class Problem:
This is NOT intended to be overloaded. Overload _presolve, _solve and
_postsolve instead.
"""
self._presolve();
t = time.time();
self._solve();
self.elapsed_time = time.time() - t;
self._postsolve();
self._presolve()
t = time.time()
self._solve()
self.elapsed_time = time.time() - t
self._postsolve()
def show(self):
"""
This procedure realizes textual and/or graphical output of the Problem's result.
......
proxtoolbox/ProxOperators/P_M.py
View file @ 2fe46b65
from proxoperators import ProxOperator,magproj
from .proxoperators import ProxOperator, magproj
import numpy as np
class P_M(ProxOperator):
"""
Projection onto Fourier magnitude constraints
"""
"""
Projection onto Fourier magnitude constraints
"""
def __init__(self,config):
"""
Initialization
def __init__(self, config):
"""
Initialization
Parameters
----------
config : dict - Dictionary containing the problem configuration. It must contain the following mapping:
'M' : array_like - nonegative real FOURIER DOMAIN CONSTRAINT
"""
self.M = config['M']
'M' : array_like - nonegative real FOURIER DOMAIN CONSTRAINT
"""
self.M = config['M']
def work(self,u):
"""
def work(self, u):
"""
Applies the proxoperator P_M
Parameters
......@@ -28,8 +29,8 @@ class P_M(ProxOperator):
Returns
-------
array_like - [p_M,phat_M] ,where p_M = the projection IN THE PHYSICAL (time) DOMAIN and phat_M = projection IN THE FOURIER DOMAIN
"""
m = self.M
a = np.fft.fft2(u)
b = magproj(a,m)
return np.fft.ifft2(b)
"""
m = self.M
a = np.fft.fft2(u)
b = magproj(a, m)
return np.fft.ifft2(b)
proxtoolbox/ProxOperators/proxoperators.py
View file @ 2fe46b65
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