Lenient extraction of corrupted imaging data #19
Conversation
I work for StandardBio, and it is a known thing that the last scan sometimes is not complete. This generates an incomplete numpy array for that acquisition. The default "read_acquisition" is called with "strict=True", but when called with "strict=False", it will use populate the missing data in the last scan with "zeros" and allow the retrieval of the acquisition.
for more information, see https://pre-commit.ci
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## develop #19 +/- ##
==========================================
Coverage ? 81.00%
==========================================
Files ? 9
Lines ? 616
Branches ? 0
==========================================
Hits ? 499
Misses ? 117
Partials ? 0 ☔ View full report in Codecov by Sentry. |
There was a problem hiding this comment.
Hi @sandip-shah
Thank you very much for contributing to this open source project! Its great to see Standard BioTools helping to facilitate Python-based data analysis. Also, @matt-sd-watson will be happy to see this PR (see #18).
I just did a first code review and have added some suggestions for changes. I'm happy to re-review this PR once these changes (especially the one regarding numpy.append) have been incorporated.
jwindhager
changed the title
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Co-authored-by: Jonas Windhager <[email protected]>
Modified np.append(data, append_data) to data = np.append(data, append_data)
|
Hey @sandip-shah, I'm currently working on some changes on your PR, I hope thats ok. One quick question: does EDIT: The unit tests answered that one. These metadata fields contain the image size, not the data indices. |
|
LGTM @sandip-shah do you agree with my changes? |
|
Hi, Yes, of course, I agree with the changes, and had made them when you suggested. Thank you for accepting the change. Sandip |
|
Hello Hello. This looks like some handy functionality! Is it part of a read_imc package release? |
|
Hi! This PR has been ready for a while now, but is still waiting for a review by @Milad4849. |
I work for StandardBio, and it is a known thing that the last scan sometimes is not complete.
This generates an incomplete numpy array for that acquisition.
The default "read_acquisition" is called with "strict=True", but when called with "strict=False", it will populate the missing data in the last scan with "zeros" and allow the retrieval of the acquisition.