Fix assay_comparison and ISS notebooks #698
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
Both notebooks had datasets where the tile shapes were not consistently provided. spacetx/slicedimage#72 broke the recording of the tile shape, and spacetx/slicedimage#73 fixes it. Test plan: `make -j run__notebooks/py/ISS_Pipeline_-_Breast_-_1_FOV.py run__notebooks/py/assay_comparison.py`
ttung
force-pushed
the
tonytung-fix-notebooks
branch
from
7fff961
to
f51e50c
Compare
Codecov Report
@@ Coverage Diff @@
## master #698 +/- ##
=======================================
Coverage 88.04% 88.04%
=======================================
Files 121 121
Lines 4132 4132
=======================================
Hits 3638 3638
Misses 494 494Continue to review full report at Codecov.
|
shanaxel42
approved these changes
Oct 11, 2018
ttung
pushed a commit
that referenced
this pull request
Oct 17, 2018
1. There is a top-level field that is `images`, and that includes both primary images and auxiliary images. Auxiliary images are addressed as <fov_object>[<image_name>]. The primary image is a special case, where the image name = "primary". 2. Updated the sptx-format schema and examples. 3. Updated the notebooks. 4. Of note is that we are _not_ deprecating 4.0.0. The format is close enough I added a read path for it! I did not convert the iss_breast full experiment data set to the new format. Fixes #625 Depends on #698 Test plan: make -j tests run_notebooks
ttung
added a commit
that referenced
this pull request
Oct 17, 2018
1. There is a top-level field that is `images`, and that includes both primary images and auxiliary images. Auxiliary images are addressed as <fov_object>[<image_name>]. The primary image is a special case, where the image name = "primary". 2. Updated the sptx-format schema and examples. 3. Updated the notebooks. 4. Of note is that we are _not_ deprecating 4.0.0. The format is close enough I added a read path for it! I did not convert the iss_breast full experiment data set to the new format. Fixes #625 Depends on #698 Test plan: make -j tests run_notebooks
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.
Both notebooks had datasets where the tile shapes were not consistently provided. spacetx/slicedimage#72 broke the recording of the tile shape, and spacetx/slicedimage#73 fixes it.
Test plan:
make -j run__notebooks/py/ISS_Pipeline_-_Breast_-_1_FOV.py run__notebooks/py/assay_comparison.py