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Rewrite MATLAB functions with matlab.io.xml.dom #346

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273 changes: 273 additions & 0 deletions scripts/trackmateEdgesR21a.m
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function trackMap = trackmateEdges(filePath, featureList)
%%TRACKMATEEDGES Import edges from a TrackMate data file.
%
% trackMap = TRACKMATEEDGES(file_path) imports the edges - or links -
% contained in the TrackMate XML file file_path. TRACKMATEEDGES only
% imports the edges of visible tracks.
%
% trackMap = TRACKMATEEDGES(file_path, feature_list) where feature_list
% is a cell array of string only imports the edge features whose names
% are in the cell array.
%
% INPUT:
%
% file_path must be a path to a TrackMate file, containing the whole
% TrackMate data, and not the simplified XML file that contains only
% linear tracks. Such simplified tracks are imported using the
% importTrackMateTracks function.
%
% A TrackMate file is a XML file that starts with the following header:
% <?xml version="1.0" encoding="UTF-8"?>
% <TrackMate version="3.3.0">
% ...
% and has a Model element in it:
% <Model spatialunits="pixel" timeunits="sec">
%
% OUTPUT:
%
% The output is a collection of tracks. trackMap is a Map that links
% track names to a MATLAB table containing the edges of this track. The
% columns of the table depend on the feature_list specified as second
% argument, but it always contains at least the SPOT_SOURCE_ID and
% SPOT_TARGET_ID features, that store the IDs of the source and target
% spots.
%
% EXAMPLE:
%
% >> trackMap = trackmateEdges(file_path);
% >> trackNames = trackMap.keys;
% >> trackNames{1}
%
% ans =
% Track_0
%
% >> trackMap('Track_0')
%
% ans =
% SPOT_SOURCE_ID SPOT_TARGET_ID DISPLACEMENT LINK_COST VELOCITY
% ______________ ______________ ____________ _________ ________
%
% 14580 16501 4.7503 1 4.7503
% 12683 14580 2.8316 1 2.8316
% 10813 12683 8.1622 1 8.1622
% 5295 7123 3.193 1 3.193
% 1715 3487 4.3063 1 4.3063
% 7123 8953 3.0804 1 3.0804
% 8953 10813 3.3689 1 3.3689
% 0 1715 6.2733 1 6.2733
% 3487 5295 5.9587 1 5.9587
%

% __
% Jean-Yves Tinevez & contributors - 2026


%% Constants definition.

TRACK_ID_ATTRIBUTE = 'TRACK_ID';
TRACK_NAME_ATTRIBUTE = 'name';
SPOT_SOURCE_ID_ATTRIBUTE = 'SPOT_SOURCE_ID';
SPOT_TARGET_ID_ATTRIBUTE = 'SPOT_TARGET_ID';

%% Retrieve edge feature list.
global isNotFirst docNode %#ok<GVMIS>
if isNotFirst
% Being called by other function
willClear = false;
else
isNotFirst = true;
willClear = true;
end
% We'll call trackmateFeatureDeclarations() to fill in table properties
% no matter what, so let's reuse that one's validation function.
try
[ ~, ef ] = trackmateFeatureDeclarationsR21a( filePath );
catch ME
throw(ME)
end

rootObj = docNode.getDocumentElement;
modelNodes = rootObj.getElementsByTagName('Model');

% Take featureList from the first <Edge> node
if nargin < 2 || isempty( featureList )
% //Edge. Why not full path?
edgeList = rootObj.getElementsByTagName( 'Edge' );
if edgeList.Length > 0
attrMap = edgeList.node(1).getAttributes;
nFeatures = attrMap.Length;
featureList = cell(nFeatures, 1);
for k = 1 : nFeatures
featureList{k} = attrMap.item(k-1).Name;
end
else
featureList = {};
end
end

frontOfList = { SPOT_SOURCE_ID_ATTRIBUTE; SPOT_TARGET_ID_ATTRIBUTE };
featureList = union(frontOfList, featureList, 'stable');
nFeatures = numel(featureList);

%% XPath to retrieve filtered track elements.
% Initialize map
trackMap = containers.Map('KeyType', 'char', 'ValueType', 'any');

% XPath: //Model/FilteredTracks/TrackID/@TrackID
fTracks = zeros(rootObj.getElementsByTagName('TrackID').Length, 1);
iTracks = 0;
for j = 1:modelNodes.Length
node = modelNodes.node(j);
% Model level
fTNode = node.getFirstElementChild;
while ~isempty(fTNode)
if strcmp('FilteredTracks', fTNode.TagName)
% FilteredTracks level
tIDNode = fTNode.getFirstElementChild;
while ~isempty(tIDNode)
if strcmp('TrackID', tIDNode.TagName)
% Found TrackID node
iTracks = iTracks + 1;
fTracks(iTracks) = ...
str2double(tIDNode.getAttribute(TRACK_ID_ATTRIBUTE));
end
tIDNode = tIDNode.getNextElementSibling;
end
end
fTNode = fTNode.getNextElementSibling;
end
end

fTracks(iTracks+1:end) = [];

if isempty(fTracks)
% No selected track, return empty map
if willClear
clear global isNotFirst docNode docNodeFileName
end
return
end

%% Read Tracks table
neTracks = rootObj.getElementsByTagName('Track').Length;
names = cell(neTracks, 1);
tracks = zeros(neTracks, 1);
iTracks = 0;
for j = 1 : modelNodes.Length
node = modelNodes.node(j);
% Model level
aTNode = node.getFirstElementChild;
while ~isempty(aTNode)
if strcmp('AllTracks', aTNode.TagName)
% AllTracks level
tNode = aTNode.getFirstElementChild;
while ~isempty(tNode)
if strcmp('Track', tNode.TagName)
% Track level
iTracks = iTracks + 1;
at = tNode.getAttributes;
names{iTracks} = at.getNamedItem(TRACK_NAME_ATTRIBUTE).Value;
tracks(iTracks) = str2double(at.getNamedItem(TRACK_ID_ATTRIBUTE).Value);
end
tNode = tNode.getNextElementSibling;
end
end
aTNode = aTNode.getNextElementSibling;
end
end
names(iTracks+1:neTracks) = [];
tracks(iTracks+1:neTracks) = [];

% Find the selected Track IDs and cache the result.
whichSel = ismember( tracks, fTracks);

%% Prepare a map: trackName -> edge table.
% Prepare metadata once
if ~isempty(whichSel)
nVNames = numel( featureList );
vDescriptions = cell( nVNames, 1);
vUnits = cell( nVNames, 1);

for l = 1 : nVNames
vn = featureList{ l };
vDescriptions{ l } = ef( vn ).name;
vUnits{ l } = ef( vn ).units;
end
else
% None of the selected tracks were found, return empty map.
if willClear
clear global isNotFirst docNode docNodeFileName
end
return
end

% Current track No.
iTracks = 0;

% XPath: (//Model/AllTracks/Track)/Edge
for j = 1 : modelNodes.Length
node = modelNodes.node(j);
% Model level
aTNode = node.getFirstElementChild;
while ~isempty(aTNode)
if strcmp('AllTracks', aTNode.TagName)
% AllTracks level
tNode = aTNode.getFirstElementChild;
while ~isempty(tNode)
if strcmp('Track', tNode.TagName)
% Track level
iTracks = iTracks + 1;
if whichSel(iTracks)
tbl = walkAndMakeTable(tNode);

tbl.Properties.DimensionNames = { 'Edge', 'Feature' };
tbl.Properties.VariableDescriptions = vDescriptions;
tbl.Properties.VariableUnits = vUnits;

trackMap( names{iTracks} ) = tbl;
end
end
tNode = tNode.getNextElementSibling;
end
end
aTNode = aTNode.getNextElementSibling;
end
end

if willClear
clear global isNotFirst docNode docNodeFileName
end

%% Subfunction.

function edgeTable = walkAndMakeTable(trackNode)
% Assuming every child element is an <Edge>...
neEdges = trackNode.getChildElementCount;
holders = cell(1, nFeatures);
for i = 1 : nFeatures
holders{i} = zeros(neEdges, 1);
end
nEdges = 0;
edgeNode = trackNode.getFirstElementChild;
while ~isempty(edgeNode)
if strcmp('Edge', edgeNode.TagName)
nEdges = nEdges+1;
attrs = edgeNode.getAttributes;
for i = 1 : nFeatures
holders{i}(nEdges) = str2double(attrs.getNamedItem(featureList{i}).Value);
end
end
edgeNode = edgeNode.getNextElementSibling;
end

% And trim the end if that turns out to be false
if nEdges < neEdges
for i = 1 : nFeatures
holders{i}(nEdges+1:end) = [];
end
end

edgeTable = table(holders{:}, 'VariableNames', featureList);
end
end

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