angelolab / segmentation / 685 / 1
81%
master: 81%

DEFAULT BRANCH: master
Ran
Files 13
Run time 2s
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 75.818% (+1.2%) from 74.648%
MPLBACKEND=Agg

push

travis-ci-com

web-flow 
Deepcell format update (#132)

* added tif output for deepcell input

* made loading from tree file-extension agnostic (no '.tif', '.tiff', etc. needed)

* reminder to add test functions for file-extension agnostisism

* moved MIBItiff loading into regular preprocessing nb and reworked channel summing

* moved deepcell input generation into data_utils to for better testing

* added test for generating deepcell input

* altered postprocessing nb

* fixed postprocessing errors

* removed legacy/watershed support from nb's, added naming options to label-tiff loading, fixed file-extension agnostisism for mixed presence

* added overlay visualization to postprocessing notebook, revised comments/structure of preprocessing nb

* fixed non-existent directory in postprocessing nb

* one weird trick

* print path

* print path in notebook

* remove import

* jupyter_path

* remove colon

* removed visualization from postprocessing nb, autosave segmentation labels xarray into label_dir

* added test function for multitiff loading

* updated file structure, removed old mibitiff preprocessing nb, and updated notebook tests

* fixed mibitiff tests, made load_imgs_from_tree error more informative

* fixed preprocessing nb

* old deepcell output folder go to bye bye land

* reworked mibi+multi tiff loading function arguments

* reworked test functions for updated mibi/multi tiff loading

* updated mibi/multi tiff loading in notebooks

* removed tiff_to_xr_labels function and replaced w/ loading from dir in postprocessing nb

* fixed postprocessing nb error

Co-authored-by: ackagel <kagelosaurus@gmail.com>
Co-authored-by: ngreenwald <noahfgreenwald@gmail.com>

718 of 947 relevant lines covered (75.82%)

0.76 hits per line

Source Files on job 685.1 (MPLBACKEND=Agg)