angelolab / ark-analysis / 2793
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Integrated plotting function (#193)

* added template function

* initial commit

* fixing visualize_watershed_transform

* fixing visualize_watershed_transform

* updated segmentation_utils and segmentation_utils_test

* updated segmentation_utils and segmentation_utils_test

* fixed indentation

* documentation

* documentation types

* Added generate channel data function

* updated

* keyerror still unresolved

* commit

* combined stuff in if statement

* message

* paths exist

* formatting

* format

* format

* consistency

* reset length settings

* Fixed comment

* comit

* line 228

* line shorter now

* documentation update

* Some documentation and cleanup

* unnecessary code deleted

* problems with replacing random_map

* Unnecessary label code removed

* deleted unnecessary params

* helper function for modifying input data

* save_tifs = all is tested

* documentation for modify_input_data

* need to reformat _generate_deepcell_ouput

* formatted

* switched out data_utils functions

* model_output removed

* plot_overlay still has problem

* documentation

* override

* comit

* comit

* Used whole_cell as index

* removed useless function

* comit

* comit

* removed unused imports

* removed model output

* docstring fixed

* documentation

* renamed visualize_segmentation

* updated documentation

* comit

* replaced generat_channel_xr

* updated mibilib version

* added low contrast warning catching

* comit

* fixed documentation and switched to fov.values

* fix new line

* overlays docu

* type error w/ visualize segmentation

* fixed type error

* merged

* Function works!

* Removed old plotting and debug statements

* cleared outputs

* merged

* added import statement

* reset nb

* reset visualization example

* removed unused methods

* just show when path is none

* save_tiffs... (continued)

1026 of 1040 relevant lines covered (98.65%)

0.99 hits per line

Jobs
ID Job ID Ran Files Coverage
1 2793.1 (MPLBACKEND=Agg) 0
98.65
 Travis Job 2793.1
Source Files on build 2793