angelolab / ark-analysis
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LAST BUILD ON BRANCH gh-readonly-queue/main/pr-958-bfc53b7d6f7bdf96ef95dd03ea84f9dfefc74dc9
branch: gh-readonly-queue/main/pr-958-bfc53b7d6f7bdf96ef95dd03ea84f9dfefc74dc9
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coverage: 93.651% (-0.1%) from 93.746%
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web-flow 
ezSegmentation (#958)

* added started ez_seg file + test

* applied filters.threshold_local's output to create a binary mask

* Adding merge_mask functionality to be later built into merge_masks notebook.

* added composite builder functionality - ready for refactoring

* ezseg_v1 notebook

* Second version of ez notebook started, changes to composite builder and mask merging, as well as new within-notebook display functionality found in ez_seg_display.py.

* Added a relabeleing step necessary for masks merging. Need to test it's mask vs channel import setup.

* refactor stage 1

refactor stage 2

* refactoring pt.2

refactor

refactor pt.3

* refactor pt. 3

* added ez_seg folder in tests

* switch order of composite builder & mask creator, added mask_name to mask creator section of notebook

* notebook adjustments

* notebook adjustments v3

* modified:   templates/ez_testing/ezseg_v2.ipynb

* refactor sections 1-3

* removed unused import

* renumber mask adjustments

* Switched ordering of mask merge and mask relabeling. Additionally updated cell table function with appropriate path names. Need to ensure this will loop through entire ez_masks to create a single table.

* Renamed the dir input to cell table creation as root_mask_dir to account for additional sources of masks.

* Composite builder now iterates over all input fov's. Bug fixed where add & subtract weren't working due to array type of uint8 (changed to int).

* Fixed problem with ez segmentation mask maker not performing size exclusion properly due to lack of boolean screen. Additionally re-wrote mask saving.

* Updated visuals for composite, mask overlay. Updated notebook with multiple different input parameters for seg. Fixed issue with segmentation process where import of a folder with one tiff could not be read into _create_object_masks.

* Updated display code and notebook cells for ez segmentation step.

* Updated ez segmentation, merging, and mask display functions.

* Fixed re... (continued)

2046 of 2281 branches covered (0.0%)

Branch coverage included in aggregate %.

356 of 369 new or added lines in 7 files covered. (96.48%)

3957 of 4129 relevant lines covered (95.83%)

5.72 hits per line

Relevant lines Covered
4129 RELEVANT LINES 3957 COVERED LINES
5.72 HITS PER LINE
Source Files on gh-readonly-queue/main/pr-958-bfc53b7d6f7bdf96ef95dd03ea84f9dfefc74dc9

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7038274386 gh-readonly-queue/main/pr-958-bfc53b7d6f7bdf96ef95dd03ea84f9dfefc74dc9 ezSegmentation (#958) * added started ez_seg file + test * applied filters.threshold_local's output to create a binary mask * Adding merge_mask functionality to be later built into merge_masks notebook. * added composite builder functionality ... push web-flow github
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