Rewrite MATLAB functions with matlab.io.xml.dom#346
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Rewrite with `matlab.io.xml.dom.*` facilities, avoiding Java heap size problems Due to shocking inefficiency of `matlab.io.xml.xpath.*`, all XPath expressions were manually transformed into tree-walking. Behaviors and calling convention remain the same - had to resort to global variables to pass the parsed XML around.
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Thanks! Is it like a complete rewrite? Or can these files be considered an update of the existing ones? In the later case, could overwrite the existing ones so that the PR shows the diff between each version of the files? |
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Rewrite with
matlab.io.xml.dom.*facilities, avoiding Java heap size problems. One path to #343.A detour from #345 - trackmateEdges requires one table per track node, but it isn't possible to express a parent node's attribute in XPath 1.0, and calling
readtable()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.It's possible to mix readtable's
trackmateSpots.minto this. Used alone it is 5x faster than walking the dom tree ourselves, but when called bytrackmateGraph.mit doubles temp memory usage, and slows things down when memory pressure kicks in.