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Merged
merged 4 commits into from
May 28, 2022
Merged

[ENH] update plotDataInRoi #42

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1f86774
update plotDataInRoi
Remi-Gau May 27, 2022
5ff89c8
add test for data in roi plotting
Remi-Gau May 27, 2022
9dc8598
refactor
Remi-Gau May 28, 2022
2ce5b6d
Merge branch 'plot' of https://github.com/cpp-lln-lab/CPP_ROI into plot
Remi-Gau May 28, 2022
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190 changes: 152 additions & 38 deletions src/roi/plotDataInRoi.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,40 @@
% Creates a figure showing a histogram of the content of a set of ROIs used on
% a set of data files.
%
% ROI label is extracted from the label entity in the BIDS filename.
%
% USAGE::
%
% figHandle = plotDataInRoi(dataImages, roiImages)
% figHandle = plotDataInRoi(dataImages, roiImages, ...
% 'scaleFactor', 1, ...
% 'roiAs', 'rows', ...
% 'dataLabel', {})
%
% :param dataImages:
% :type dataImages: path or cellstr of paths
%
% :param roiImages:
% :type roiImages: path or cellstr of paths
%
% :param scaleFactor: value to scale the factor by. Default to 1.
% :type scaleFactor: numerical
%
% :param roiAs: Determine if the ROI are supposed to be organized by rows or
% columns.
% Default to 'rows'.
% :type roiAs: 'rows' or 'cols'
%
% :param dataLabel: strings to use to label the data rows or columns.
% :type dataLabel: cellstr
%
% :param maxVox: max of scale for nb of voxels. Default to [].
% :type maxVox: positive integer
%
% :param nbBins: use the same number of bins for all graphs.
% By default based on the number of unique values across all
% the datasets.
% :type nbBins: positive integer
%
%
% EXAMPLE::
%
Expand All @@ -33,16 +57,26 @@
defaultNbBins = 100;

isFile = @(x) iscellstr(x) || exist(x, 'file') == 2;
rowOrCol = @(x) ismember(x, {'rows', 'cols'});

args = inputParser;

args.addRequired('dataImages', isFile);
args.addRequired('roiImages', isFile);
args.addParameter('scaleFactor', 1, @isnumeric);
args.addParameter('roiAs', 'rows', rowOrCol);
args.addParameter('dataLabel', {}, @iscellstr);
args.addParameter('maxVox', [], @isnumeric);
args.addParameter('nbBins', [], @isnumeric);

args.parse(varargin{:});

dataImages = args.Results.dataImages;
roiImages = args.Results.roiImages;
scaleFactor = args.Results.scaleFactor;
roiAs = args.Results.roiAs;
dataLabel = args.Results.dataLabel;
nbBins = args.Results.nbBins;

if ischar(dataImages)
dataImages = {dataImages};
Expand All @@ -55,85 +89,100 @@
nbRois = numel(roiImages);
nbData = numel(dataImages);

if nbRois == 1 || nbData == 1
[rows, cols] = optimizeSubplotNumber(nbRois * nbData);
else
if numel(dataLabel) ~= nbData
warning('numel dataLabel must be equal to numel dataImages');
dataLabel = {};
end

if strcmp(roiAs, 'rows')
rows = nbRois;
cols = nbData;
elseif strcmp(roiAs, 'cols')
cols = nbRois;
rows = nbData;
end

figHandle = figure('position', [50 50 300 * rows 300 * cols]);
figHandle = figure('position', [50 50 300 * cols 300 * rows]);

%% collect info to adapt the graphs later on

% y scale
maxVox = [];
nbBinsList = [];

% x axis
% limit axis of axis for ROI (nb of voxels)
MIN = [];
MAX = [];

% use the same number of bins for all graphs
% based on the minimum number of unique values across all the datasets
nbBins = [];

% to plot all the modes
modes = [];

subplotList = [];

idxSubplot = 1;

for iRoi = 1:nbRois
for iRow = 1:rows

for iData = 1:nbData
for iCol = 1:cols

data{idxSubplot} = spm_summarise(spm_vol(dataImages{iData}), roiImages{iRoi});
if strcmp(roiAs, 'rows')
data{idxSubplot} = spm_summarise(spm_vol(dataImages{iCol}), roiImages{iRow}) * scaleFactor;
elseif strcmp(roiAs, 'cols')
data{idxSubplot} = spm_summarise(spm_vol(dataImages{iRow}), roiImages{iCol}) * scaleFactor;
end

[~, bins] = hist(data{idxSubplot}, defaultNbBins);
if isempty(data{idxSubplot})
bins = nan;
else
[~, bins] = hist(data{idxSubplot}, defaultNbBins);
end
MAX(end + 1) = max(bins);
MIN(end + 1) = min(bins);

% modes and nbBins work better on rounded values
modes(end + 1) = mode(round(data{idxSubplot}));
nbBins(end + 1) = numel(unique(round(data{idxSubplot})));
nbBinsList(end + 1) = numel(unique(round(data{idxSubplot})));

subplotList(iRoi, iData) = idxSubplot;
subplotList(iRow, iCol) = idxSubplot;

idxSubplot = idxSubplot + 1;

end

end

nbBins = min(nbBins);

for i = 1:numel(data)
tmp = hist(data{i}, nbBins);
maxVox(end + 1) = max(tmp);
if isempty(nbBins)
nbBins = max(nbBinsList);
end

maxVox = getMaxVox(args, data);

%% plot histogram and mode

idxSubplot = 1;

for iRoi = 1:nbRois
for iRow = 1:rows

for iData = 1:nbData
for iCol = 1:cols

subplot(rows, cols, idxSubplot);

hold on;

hist(data{idxSubplot}, nbBins);
if ~isempty(data{idxSubplot})

hist(data{idxSubplot}, nbBins);

plot([modes(idxSubplot) modes(idxSubplot)], ...
[0 max(maxVox)], ...
'--r', ...
'linewidth', 1);
plot([modes(idxSubplot) modes(idxSubplot)], ...
[0 max(maxVox)], ...
'--r', ...
'linewidth', 1);

bf = bids.File(roiImages{iRoi});
title(['roi: ' bf.entities.label]);
t = text(max(MAX) * 0.5, ...
max(maxVox) * 0.85, ...
sprintf('mean=%0.2f', mean(data{idxSubplot})));

set(t, 'FontSize', 10);

end

axis([min(MIN) max(MAX) 0 max(maxVox)]);

Expand All @@ -143,14 +192,79 @@

end

for i = 1:cols
subplot(rows, cols, subplotList(end, i));
xlabel('intensities');
labelAxis(roiAs, rows, cols, subplotList, roiImages, dataLabel);

end

function labelAxis(roiAs, rows, cols, subplotList, roiImages, dataLabel)

if strcmp(roiAs, 'rows')

for i = 1:cols
subplot(rows, cols, subplotList(end, i));
xlabel('intensities');
end

for i = 1:rows

subplot(rows, cols, subplotList(i, 1));

bf = bids.File(roiImages{i});
l = ylabel(sprintf('roi: %s\nnb voxels', bf.entities.label));
set(l, 'FontWeight', 'bold');

end

else

for i = 1:cols

subplot(rows, cols, subplotList(1, i));

bf = bids.File(roiImages{i});
title(sprintf('roi: %s', bf.entities.label));

subplot(rows, cols, subplotList(end, i));

xlabel('nb voxels');

end

for i = 1:rows

subplot(rows, cols, subplotList(i, 1));

label = '';
if ~isempty(dataLabel)
label = dataLabel{i};
end
l = ylabel(sprintf('%s', label));
set(l, 'FontWeight', 'bold');

end

end

for i = 1:rows
subplot(rows, cols, subplotList(i, 1));
ylabel('nb voxels');
end

function maxVox = getMaxVox(args, data)

maxVox = args.Results.maxVox;

if isempty(maxVox)

for i = 1:numel(data)

tmp = hist(data{i}, nbBins);

if isempty(tmp)
maxVox(end + 1) = nan;
else
maxVox(end + 1) = max(tmp);
end

end

end

end
20 changes: 20 additions & 0 deletions tests/test_plotRoi.m
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,26 @@ function test_test_plotDataInRoi_many_rois_and_data()

end

function test_test_plotDataInRoi_many_rois_as_cols_and_data()

mask1 = createDummyMask(1);
mask2 = createDummyMask(2);
mask3 = createDummyMask(3);
mask4 = createDummyMask(4);
data1 = createDummyData(1);
data2 = createDummyData(2);
data3 = createDummyData(3);
data4 = createDummyData(4);

mask = cellstr(cat(1, mask1, mask2, mask3, mask4));
data = cellstr(cat(1, data1, data2, data3, data4));

plotDataInRoi(data, mask, 'roiAs', 'cols');

delete *.nii;

end

function M = mat()
M = ...
[-3 0 0 84; ...
Expand Down