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Rewrite MATLAB import functions with readstruct() #350

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9e5c3e0
Rewrite with readstruct()
Jerry1144 Jun 19, 2026
8c41ad1
Fix aliased timer variable
Jerry1144 Jun 19, 2026
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120 changes: 58 additions & 62 deletions scripts/importTrackMateTracks.m
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,14 @@
% </particle>
% ...
% </Tracks>
%
%
% Jean-Yves Tinevez <jeanyves.tinevez@gmail.com> - 2013


% __
% Jean-Yves Tinevez & contributors - 2026

%% Constants definition.

ATTRIBUTE_SUFFIX = "__";

%% Input

Expand All @@ -81,80 +86,71 @@
%% Load and Test compliance

try
doc = xmlread(file);
catch %#ok<CTCH>
error('Failed to read XML file %s.',file);
end

root = doc.getDocumentElement;

if ~strcmp(root.getTagName, 'Tracks')
error('MATLAB:importTrackMateTracks:BadXMLFile', ...
'File does not seem to be a proper track file.')
rootStruct = readstruct(file, "FileType", "xml", "StructSelector", "/Tracks", ...
"ImportAttributes", true, "AttributeSuffix", ATTRIBUTE_SUFFIX);
catch ME
switch ME.identifier
case 'MATLAB:UndefinedFunction'
error("Your MATLAB is too old (pre-R2021a) to run this script.");
case 'MATLAB:nonExistentField'
error('MATLAB:importTrackMateTracks:BadXMLFile', ...
"File does not seem to be a proper track file.");
otherwise
error(ME.identifier, "Failed to read XML file %s.", file);
end
end

%% Get metadata
metadata.spaceUnits = char( root.getAttribute('spaceUnits') );
metadata.timeUnits = char( root.getAttribute('timeUnits') );
metadata.frameInterval = str2double( root.getAttribute('frameInterval') );
metadata.date = char( root.getAttribute('generationDateTime') );
metadata.source = char( root.getAttribute('from') );
metadata.spaceUnits = char(rootStruct.("spaceUnits"+ATTRIBUTE_SUFFIX));
metadata.timeUnits = char(rootStruct.("timeUnits"+ATTRIBUTE_SUFFIX));
metadata.frameInterval = rootStruct.("frameInterval"+ATTRIBUTE_SUFFIX);
if ~isa(metadata.frameInterval, "double")
metadata.frameInterval = double(metadata.frameInterval); end
% readstruct() recognizes date and transforms into Datetime. Probably need
% a datefmt argument here
metadata.date = char(rootStruct.("generationDateTime"+ATTRIBUTE_SUFFIX));
metadata.source = char(rootStruct.("from"+ATTRIBUTE_SUFFIX));


%% Scale time using physical units if required

% NaN is not greater than zero
willScaleT = scalet && metadata.frameInterval > 0;

%% Parse

nTracks = str2double( root.getAttribute('nTracks') );
nTracks = rootStruct.("nTracks"+ATTRIBUTE_SUFFIX);
if ~isa(nTracks, "double"); nTracks = double(nTracks); end
tracks = cell(nTracks, 1);
trackNodes = root.getElementsByTagName('particle');
trackNodes = rootStruct.particle(1:nTracks);

for i = 1 : nTracks

trackNode = trackNodes.item(i-1);
detectionNodes = trackNode.getElementsByTagName('detection');

nSpots = str2double( trackNode.getAttribute('nSpots') );
nSpots = min( nSpots, detectionNodes.getLength() );
trackNode = trackNodes(i);
detectionNodes = trackNode.detection;

A = NaN( nSpots, 4); % T, X, Y, Z
nSpots = double(trackNode.("nSpots"+ATTRIBUTE_SUFFIX));
nSpots = min( nSpots, numel(detectionNodes) );
detectionNodes = detectionNodes(1:nSpots);

for j = 1 : nSpots

detectionNode = detectionNodes.item(j-1);
t = str2double(detectionNode.getAttribute('t'));
x = str2double(detectionNode.getAttribute('x'));
y = str2double(detectionNode.getAttribute('y'));
z = str2double(detectionNode.getAttribute('z'));
A(j, :) = [ t x y z ];

t = [detectionNodes.("t"+ATTRIBUTE_SUFFIX)];
if ~isa(t, "double"); t = double(t); end
x = [detectionNodes.("x"+ATTRIBUTE_SUFFIX)];
if ~isa(x, "double"); x = double(x); end
y = [detectionNodes.("y"+ATTRIBUTE_SUFFIX)];
if ~isa(y, "double"); y = double(y); end
z = [detectionNodes.("z"+ATTRIBUTE_SUFFIX)];
if ~isa(z, "double"); z = double(z); end

if willScaleT
t = t * metadata.frameInterval;
end

tracks{i} = A;

end

%% Clip Z dimension if possible and asked

if clipz

if all(cellfun(@(X) all( X(:,4) == 0), tracks))

if clipz && all(z == 0)
% Remove the z coordinates since it is 0 everywhere
for i = 1 : nTracks
tracks{i} = tracks{i}(:, 1:3);
end
end

end

%% Scale time using physical units if required

if scalet
if ~isnan(metadata.frameInterval) && metadata.frameInterval > 0

% Scale time so that it is in physical units
for i = 1 : nTracks
tracks{i}(:, 1) = tracks{i}(:, 1) * metadata.frameInterval;
end

tracks{i} = [t(:) x(:) y(:)];
else
tracks{i} = [t(:) x(:) y(:) z(:)];
end

end
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