Additional builders for BinaryMaskCollection #1637
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
changed the base branch from
tonytung-label-image-vocabulary
to
tonytung-coordinate-cleanup
Codecov Report
@@ Coverage Diff @@
## tonytung-uncrop #1637 +/- ##
===================================================
+ Coverage 89.74% 90.11% +0.36%
===================================================
Files 220 222 +2
Lines 8290 8578 +288
===================================================
+ Hits 7440 7730 +290
+ Misses 850 848 -2
Continue to review full report at Codecov.
|
ttung
force-pushed
the
tonytung-coordinate-cleanup
branch
from
26894de to
ecc5a1c
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
3 times, most recently
from
a7293da to
b47d603
Compare
ttung
force-pushed
the
tonytung-coordinate-cleanup
branch
from
765b842 to
c60458d
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
3 times, most recently
from
88778bd to
746eaa2
Compare
ttung
changed the base branch from
tonytung-coordinate-cleanup
to
tonytung-uncrop
ttung
force-pushed
the
tonytung-uncrop
branch
from
0ab6a76 to
6f104cb
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
746eaa2 to
5f4680c
Compare
shanaxel42
approved these changes
Nov 12, 2019
ttung
force-pushed
the
tonytung-uncrop
branch
from
6f104cb to
cefb28b
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
5f4680c to
0b6a4dc
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
cefb28b to
eb49e05
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
0b6a4dc to
8669973
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
eb49e05 to
c44608b
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
8669973 to
a65f7cd
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
c44608b to
6e3f361
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
3 times, most recently
from
75c46b5 to
7516dd2
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
2e197eb to
cc14f03
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
3 times, most recently
from
d85eb1e to
de76069
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
fd63cdb to
922f2be
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
2 times, most recently
from
6276179 to
d05355b
Compare
ttung
force-pushed
the
tonytung-uncrop
branch
from
5806efa to
7339bfd
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
2 times, most recently
from
4632f85 to
ead1f9c
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
2 times, most recently
from
45e7a41 to
f66bca2
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
f66bca2 to
7ce3d9c
Compare
ttung
force-pushed
the
tonytung-additional-builders
branch
from
7ce3d9c to
7b732a9
Compare
1. `from_binary_arrays_and_ticks` will allow morphological filters to take a set of binary masks, run some processing, and produce another set of binary masks. 2. `from_label_array_and_ticks` will allow image processing tools that produce a labeled image and produce a set of binary masks. `skimage.feature.watershed` is an example of (2), and indeed, we adapt the existing watershed output to use `from_label_array_and_ticks` Test plan: pass travis, but mostly `make -j lint mypy && pytest -v -n4 starfish/core/morphology/object/` Depends on #1632
ttung
force-pushed
the
tonytung-additional-builders
branch
from
7b732a9 to
36672e7
Compare
ttung
pushed a commit
that referenced
this pull request
Nov 18, 2019
Methods to create label arrays, binary arrays, and binary masks. This is mostly to reduce a bit of copy pasta, and to make it easier to write simple examples in docblocks. Depends on #1637 Test plan: pytest starfish/core/morphology/object/binary_mask/test/
ttung
pushed a commit
that referenced
this pull request
Dec 5, 2019
BinarizeImage takes an ImageStack and binarizes it into a BinaryMaskCollection. Depends on #1637 Test plan: add tests for simple binarizing, and to test the input requirements.
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.
from_binary_arrays_and_tickswill allow morphological filters to take a set of binary masks, run some processing, and produce another set of binary masks.from_label_array_and_tickswill allow image processing tools that produce a labeled image and produce a set of binary masks.skimage.feature.watershedis an example of (2), and indeed, we adapt the existing watershed output to usefrom_label_array_and_ticksTest plan: pass travis, but mostly
make -j lint mypy && pytest -v -n4 starfish/core/morphology/object/Depends on #1647