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[ENH] add input validation #90

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Merged
merged 2 commits into from
Feb 17, 2023
Merged

[ENH] add input validation #90

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254b7eb
add input validation
Remi-Gau Feb 17, 2023
6b74c01
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 17, 2023
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1 change: 1 addition & 0 deletions src/atlas/extractRoiByLabel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
%
% :param sourceImage: discrete segmentation source image fullpath
% :type sourceImage: string
%
% :param labelStruct: 1x1 structure with fields ``ROI`` for the ROI name
% and ``label`` for the corresponding label
% :type labelStruct: structure
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37 changes: 30 additions & 7 deletions src/atlas/extractRoiFromAtlas.m
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
function roiImage = extractRoiFromAtlas(outputDir, atlasName, roiName, hemisphere)
function roiImage = extractRoiFromAtlas(varargin)
%
% Outputs a ROI image and side car json for a given atlas, roi name (as
% defined in the look up table of that atlas) and a hemisphere
Expand All @@ -8,22 +8,45 @@
% roiImage = extractRoiFromAtlas(outputDir, atlasName, roiName, hemisphere)
%
% :param outputDir:
% :param atlasName: ``'wang'``, ``'visfatlas'``, ``'neuromorphometrics'``, ``'hcpex'``
% :param roiName: run ``getLookUpTable(atlasName)`` to get a list of ROI names to choose from
% :param hemisphere: ``L`` or ``R``
% :type outputDir: string
%
% :param atlasName: ``'wang'``, ``'visfatlas'``, ``'neuromorphometrics'``, ``'hcpex'``
% :type atlasName: string
%
% :param roiName: run ``getLookUpTable(atlasName)`` to get a list of ROI names to choose from
% :type roiName: string
%
% :param hemisphere: ``L`` or ``R``
% :type hemisphere: string
%
%
% EXAMPLE::
%
% outputDir = pwd;
% atlasName = 'neuromorphometrics';
% roiName = 'PCu precuneus';
% hemisphere = 'R';
%
% extractRoiFromAtlas(outputDir, atlasName, roiName, hemisphere)
%

% (C) Copyright 2021 CPP ROI developers

if ~ismember(hemisphere, {'L', 'R'})
isChar = @(x) ischar(x);

error('\n Hemisphere label %s not valid, try "L" or "R"', hemisphere);
args = inputParser;

end
addRequired(args, 'outputDir', isChar);
addRequired(args, 'atlasName', @isAKnownAtlas);
addRequired(args, 'roiName', isChar);
addRequired(args, 'hemisphere', @(x) ismember(x, {'L', 'R'}));

parse(args, varargin{:});

outputDir = args.Results.outputDir;
atlasName = args.Results.atlasName;
roiName = args.Results.roiName;
hemisphere = args.Results.hemisphere;

[atlasFile, lut] = getAtlasAndLut(atlasName);

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