Rewrite MATLAB functions with matlab.io.xml.dom.*#351
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Circumvent Java heap size problems with recent MATLAB dealing with large XML. MATLAB's `io.xml.xpath.*` appears to execute eagerly and over-consumes memory Walking the dom tree ourselves is slower than native `readtable()` when every sub-node are consolidated into one big table, but the latter cannot easily handle "one edge table per track" which is required by trackmateEdges.m Also replaced every `str2double` with `double(string())` per recommendation.
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Rewrite with matlab.io.xml.dom.* facilities, avoiding Java heap size problems. Available since R2021a. One path to #343. Force-push of #346
A detour from #345 -
trackmateEdgesrequires one table per track node, but it isn't possible to express a parent node's attribute in XPath 1.0, and callingreadtable()once per track is slow (50+h from my 16k track file).Then, to keep the total memory use in check, all function in the series must adhere to a single path. Apparently memory reuse does not happen across
readstruct,readtable, andmatlab.io.xml.*, and GC only occurs during inactivity. Thus the total rewrite.Finally, I eliminated all calls to
str2double(one function call for each attribute for each node!), replacing them with the weird-lookingdouble(string())per Mathworks recommendation. Speed up is very significant. I also changed text preallocation tostrings, with no noticeable impact.PS: Text comparison still uses
strcmp, which is faster than string's==.PPS: Why text preallocation using
stringsnot brings improvements, is beyond me. I changed that only for aesthetic reasons.