Rewrite MATLAB import functions with readtable()#345
Open
Jerry1144 wants to merge 4 commits into
Open
Conversation
Rewritten trackmateSpots.m with `readtable()` function. To support its function, trackmateFeatureDeclarations.m is rewritten too. Shifting to MATLAB's own capabilities helps alleviate heap size problems.
Fix bug: switch should work on MException's identifier.
This was referenced Jun 2, 2026
Each track is read once with readtable(). Very slow and memory hungry. Owing to XPath 1.0's limitations, it's not possible to record the parent node when a child node is selected. Thus the obviously efficient solution of reading once and sub-dividing later cannot be taken.
Minor changes to call *R21a.m functions.
Jerry1144
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Another path to #343, rewriting trackmateSpots.m with
readtable()function. Shifting to MATLAB's own capabilities helps alleviate Java heap size problems.Specific to this path:
trackmateFeatureDeclarations.mfor the initial validity check, and directly construct XMLImportOptions instead of calling detectImportOptions() where possible.detectImportOptions(). Instead I consult the feature map. Doing so shaves off ~15% run time and 10GB memory use(!)