Optimize pyimzml.ImzMLParser to handle much larger data files
#23
Conversation
This file contains 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
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
Pull Request Test Coverage Report for Build 8976071893Details
💛 - Coveralls |
|
Closing out this PR, the updated spectra extractor removes the need to support |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
What is the purpose of this PR?
For large MALDI runs, it is not uncommon for the data in
.imzMLfiles to exceed the amount of memory on the MALDI machine. The baseimzmlextractor does not handle this, so our existing forked installation needs to be used instead.How did you implement your changes
Forked
pyimzmland update to remove unnecessary processing for our purposes, and clear out each element seen byiterparseonce fully processed.Remaining issues
Further testing is needed.