angelolab / segmentation / 685
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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

Jobs
ID Job ID Ran Files Coverage
1 685.1 (MPLBACKEND=Agg) 0
75.82
 Travis Job 685.1
Source Files on build 685
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