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added missing functions to searchlight scripts #31

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Merged
merged 7 commits into from
Jul 24, 2018
Merged

added missing functions to searchlight scripts #31

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a09f2e3
Edit the color bar setting
yunshiuan Mar 1, 2018
614ef81
Merge pull request #25 from yunshiuan/develop
caiw Mar 4, 2018
d535bfe
Merge pull request #26 from rsagroup/master
caiw Mar 8, 2018
cfd3f3d
Fixed typo.
caiw Mar 21, 2018
29fe778
Enable dotSize in the MDS plot to be adjustable
yunshiuan Mar 31, 2018
f1ed1de
Merge pull request #28 from yunshiuan/develop
caiw Apr 2, 2018
63ed037
Merge branch 'master' into develop
caiw May 19, 2018
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18 changes: 9 additions & 9 deletions +rsa/+fig/figureMDSArrangement.m
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Original file line number Diff line number Diff line change
Expand Up @@ -93,13 +93,13 @@ function figureMDSArrangement(RDM, userOptions, localOptions)
%__________________________________________________________________________
% Copyright (C) 2010 Medical Research Council

import rsa.*
import rsa.fig.*
import rsa.fmri.*
import rsa.rdm.*
import rsa.sim.*
import rsa.spm.*
import rsa.stat.*
import rsa.*
import rsa.fig.*
import rsa.fmri.*
import rsa.rdm.*
import rsa.sim.*
import rsa.spm.*
import rsa.stat.*
import rsa.util.*

%% define defaults
Expand Down Expand Up @@ -172,8 +172,8 @@ function figureMDSArrangement(RDM, userOptions, localOptions)
% categories undefined: plot all text labels in black
veryLocalOptions.textLabels = localOptions.textLabels;
veryLocalOptions.dotColours = localOptions.dotColours;
if isfield(localOptions, 'dotSize')
veryLocalOptions.dotSize = localOptions.dotSize;
if isfield(userOptions, 'dotSize')
veryLocalOptions.dotSize = userOptions.dotSize;
end%if
plotDotsWithTextLabels(pats_mds_2D,veryLocalOptions);

Expand Down
2 changes: 1 addition & 1 deletion +rsa/+fmri/fMRIDataPreparation.m
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Expand Up @@ -69,7 +69,7 @@
if ~isfield(userOptions, 'rootPath'), error('fMRIDataPreparation:NoRootPath', 'rootPath must be set. See help'); end%if
if ~isfield(userOptions, 'betaPath'), error('fMRIDataPreparation:NoBetaPath', 'betaPath must be set. See help'); end%if
if ~isfield(userOptions, 'subjectNames'), error('fMRIDataPreparation:NoSubjectNames', 'subjectNames must be set. See help'); end%if
if (~isfield(userOptions, 'conditionLabels') && ischar(betaCorrespondence) && strcpmi(betaCorrespondence, 'SPM')), error('fMRIDataPreparation:NoConditionLabels', 'conditionLables must be set if the data is being extracted from SPM.'); end%if
if (~isfield(userOptions, 'conditionLabels') && ischar(betaCorrespondence) && strcmpi(betaCorrespondence, 'SPM')), error('fMRIDataPreparation:NoConditionLabels', 'conditionLables must be set if the data is being extracted from SPM.'); end%if

% The filenames contain the analysisName as specified in the user options file
ImageDataFilename = [userOptions.analysisName, '_ImageData.mat'];
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30 changes: 20 additions & 10 deletions +rsa/figureRDMs.m
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Expand Up @@ -33,7 +33,10 @@ function figureRDMs(RDMs, userOptions, localOptions)
% ranks preserved. If false, true values are represented.
% Defaults to true. This is for display only.
% userOptions.colourScheme
% A colour scheme for the RDMs. Defualts to jet(64).
% A colour scheme for the RDMs. For Matlab version
% before R2015b,
% defualts to jet(64); for versions afterward,
% defaults to colormap(jet(256)).
%
% localOptions --- Further options.
% localOptions.figureNumber
Expand All @@ -48,17 +51,24 @@ function figureRDMs(RDMs, userOptions, localOptions)
%__________________________________________________________________________
% Copyright (C) 2010 Medical Research Council

import rsa.*
import rsa.fig.*
import rsa.fmri.*
import rsa.rdm.*
import rsa.sim.*
import rsa.spm.*
import rsa.stat.*
import rsa.*
import rsa.fig.*
import rsa.fmri.*
import rsa.rdm.*
import rsa.sim.*
import rsa.spm.*
import rsa.stat.*
import rsa.util.*

returnHere = pwd;

% Detect Matlab version (R2015b changes default color maps: should use
% colormap() to specify the color of the color bar.
matlabVersion = str2num(cell2mat(regexp(version('-release'),'\d+','match')));
if matlabVersion>2015
color=colormap(jet(256));
else
color=jet(64);
end
%% Set defaults and check options struct
if nargin == 2, localOptions = struct(); end%if:nargin
if ~isfield(userOptions, 'analysisName'), error('figureInterleavedRDMs:NoAnalysisName', 'analysisName must be set. See help'); end%if
Expand All @@ -68,7 +78,7 @@ function figureRDMs(RDMs, userOptions, localOptions)
userOptions = setIfUnset(userOptions, 'saveFigureFig', false);
userOptions = setIfUnset(userOptions, 'displayFigures', true);
userOptions = setIfUnset(userOptions, 'rankTransform', true);
userOptions = setIfUnset(userOptions, 'colourScheme', jet(64));
userOptions = setIfUnset(userOptions, 'colourScheme', color);

if ~isfield(userOptions,'dpi'), userOptions.dpi=300; end;
if ~isfield(userOptions,'tightInset')
Expand Down