Refactor blobs_image api. #1143
Merged
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
ttung
force-pushed
the
tonytung-blobs-image
branch
from
bafdf4c to
3b1cc1e
Compare
Codecov Report
@@ Coverage Diff @@
## master #1143 +/- ##
==========================================
+ Coverage 88.62% 88.63% +<.01%
==========================================
Files 130 130
Lines 4642 4637 -5
==========================================
- Hits 4114 4110 -4
+ Misses 528 527 -1
Continue to review full report at Codecov.
|
ambrosejcarr
approved these changes
Apr 8, 2019
… arrays. 1. blobs_image is, at the user's interaction level, an ImageStack. Internally, `starfish.spots._detector.detect.detect_spots` will convert it to a numpy array. This is to allow the code path where we don't have a reference image to continue taking advantage of ImageStack's apply/transform logic. 2. Because the way we generate the blobs_image (max projection) happens on different axes, it must be explicitly provided to `detect_spots`. 3. Other small and insignificant changes. Test plan: `make -j test run_notebooks`
ttung
force-pushed
the
tonytung-blobs-image
branch
from
3b1cc1e to
19c5d18
Compare
ttung
added a commit
that referenced
this pull request
Apr 8, 2019
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Outdated suggestions cannot be applied.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.
High level goal: detect spots should accept imagestacks and not numpy arrays.
starfish.spots._detector.detect.detect_spotswill convert it to a numpy array. This is to allow the code path where we don't have a reference image to continue taking advantage of ImageStack's apply/transform logic.detect_spots.Test plan:
make -j test run_notebooks