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Merge pull request #73 from ICB-DCM/release-1.0
Release 1.0 beta
2 parents 737faf6 + be84919 commit 422f213

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‎.gitignore‎

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doc/config/Doxyfile
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doc/config/latexextras.sty
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doc/config/mtocpp_filter.sh
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DRAMToolbox
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*.asv
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‎@DRAMOptions/DRAMOptions.m‎

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% @file DRAMOptions
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% @brief A class for sanity checks of DRAM algorithm (MCMC samling) in PESTO
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classdef DRAMOptions < matlab.mixin.SetGet
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% DRAMOptions provides an option container to pass options as subclass
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% into the PestoSamplingOptions class.
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%
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% This file is based on AMICI amioptions.m (http://icb-dcm.github.io/AMICI/)
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properties
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%% Delayed Rejection Adaption Metropolis options
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% Note: This algorithm uses a delayed rejection scheme for better mixing.
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% --- Delayed Rejection Adaptive Metropolis ---
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% opt.DRAM.regFactor : This factor is used for regularization in
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% cases where the single-chain proposal
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% covariance matrices are ill conditioned.
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% Larger values equal stronger
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% regularization.
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% opt.DRAM.nTry : The number of tries in the delayed
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% rejection scheme
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% opt.DRAM.verbosityMode : Defines the level of verbosity 'silent', 'visual',
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% 'debug' or 'text'
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% opt.DRAM.adaptionInterval : Updates the proposal density only every opt.DRAM.adaptionInterval
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% time
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regFactor = 1e-6;
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nTry = 1;
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verbosityMode = 'text';
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adaptionInterval = 1;
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end
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properties (Hidden)
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end
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methods
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function obj = DRAMOptions(varargin)
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% DRAMOptions Construct a new DRAMOptions object
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%
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% OPTS = DRAMOptions() creates a set of options with
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% each option set to itsdefault value.
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%
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% OPTS = DRAMOptions(PARAM, VAL, ...) creates a set
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% of options with the named parameters altered with the
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% specified values.
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%
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% OPTS = DRAMOptions(OLDOPTS, PARAM, VAL, ...)
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% creates a copy of OLDOPTS with the named parameters altered
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% with the specified value
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%
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% Note to see the parameters, check the
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% documentation page for DRAMOptions
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% adapted from SolverOptions
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if nargin > 0
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% Deal with the case where the first input to the
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% constructor is a amioptions/struct object.
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if isa(varargin{1},'DRAMOptions')
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if strcmp(class(varargin{1}),class(obj))
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obj = varargin{1};
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else
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% Get the properties from options object passed
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% into the constructor.
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thisProps = properties(obj);
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% Set the common properties. Note that we
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% investigated first finding the properties that
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% are common to both objects and just looping over
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% those. We found that in most cases this was no
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% quicker than just looping over the properties of
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% the object passed in.
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for i = 1:length(thisProps)
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try %#ok
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% Try to set one of the properties of the
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% old object in the new one.
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obj.(thisProps{i}) = varargin{1}.(thisProps{i});
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end
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end
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end
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firstInputObj = true;
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elseif isstruct(varargin{1})
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fieldlist = fieldnames(varargin{1});
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for ifield = 1:length(fieldlist)
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obj.(fieldlist{ifield}) = varargin{1}.(fieldlist{ifield});
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end
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firstInputObj = true;
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elseif isempty(varargin{1})
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firstInputObj = true;
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else
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firstInputObj = false;
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end
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% Extract the options that the caller of the constructor
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% wants to set.
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if firstInputObj
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pvPairs = varargin(2:end);
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else
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pvPairs = varargin;
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end
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% Loop through each param-value pair and just try to set
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% the option. When the option has been fully specified with
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% the correct case, this is fast. The catch clause deals
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% with partial matches or errors.
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haveCreatedInputParser = false;
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for i = 1:2:length(pvPairs)
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try
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obj.(pvPairs{i}) = pvPairs{i+1};
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catch ME %#ok
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% Create the input parser if we haven't already. We
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% do it here to avoid creating it if possible, as
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% it is slow to set up.
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if ~haveCreatedInputParser
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ip = inputParser;
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% Structures are currently not supported as
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% an input to optimoptions. Setting the
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% StructExpand property of the input parser to
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% false, forces the parser to treat the
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% structure as a single input and not a set of
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% param-value pairs.
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ip.StructExpand = false;
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% Get list of option names
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allOptionNames = properties(obj);
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for j = 1:length(allOptionNames)
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% Just specify an empty default as we already have the
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% defaults in the options object.
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ip.addParameter(allOptionNames{j}, []);
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end
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haveCreatedInputParser = true;
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end
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% Get the p-v pair to parse.
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thisPair = pvPairs(i:min(i+1, length(pvPairs)));
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ip.parse(thisPair{:});
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% Determine the option that was specified in p-v pairs.
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% These options will now be matched even if only partially
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% specified (by 13a). Now set the specified value in the
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% options object.
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optionSet = setdiff(allOptionNames, ip.UsingDefaults);
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obj.(optionSet{1}) = ip.Results.(optionSet{1});
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end
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end
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end
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end
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function new = copy(this)
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new = feval(class(this));
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p = properties(this);
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for i = 1:length(p)
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new.(p{i}) = this.(p{i});
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end
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end
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%% Part for checking the correct setting of options
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function set.regFactor(this, value)
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if(isnumeric(value) && value > 0)
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this.regFactor = lower(value);
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else
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error(['Please specify a positive regularization factor for ill conditioned covariance'...
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' matrices of the adapted proposal density, e.g. ' ...
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'PestoSamplingOptions.DRAM.regFactor = 1e-5']);
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end
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end
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function set.nTry(this, value)
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if(isnumeric(value) && value > 0)
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this.nTry = lower(value);
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else
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error(['Please specify a positive number of maximum tries, e.g. ' ...
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'PestoSamplingOptions.DRAM.nTry = 3']);
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end
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end
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function set.verbosityMode(this, value)
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if (strcmp(value, 'text') || strcmp(value, 'silent') || strcmp(value, 'debug'))
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this.verbosityMode = lower(value);
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else
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error(['Please specify a verbosity mode, e.g. ' ...
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'PestoSamplingOptions.DRAM.verbosityMode = "text"']);
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end
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end
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function set.adaptionInterval(this, value)
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if(isnumeric(value) && value > 0)
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this.adaptionInterval = lower(value);
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else
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error(['Please specify the adaption inteval, e.g. ' ...
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'PestoSamplingOptions.DRAM.adaptionInterval = 1']);
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end
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end
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end
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end
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