angelolab / segmentation / 938
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Synthetic spatial data generation: Part 2 (channel-based) (#122)

* Remove unnecessary comment, mostly for creating a new PR

* Reorganize functions so generate_random_cell_shapes can easily integrate with existing code

* Add code to generate ellipses and visualize them in a format compatible with Ellipse in matplotlib.patches

* PEP8 fix in visualize

* matplotlib fixes

* After a bunch of overengineered ideas settle for a basic implementation of generating segmentation masks and add stub for test channel data

* Add a function to generate just two segmentation masks, still figuring out membrane and channel extraction

* Handle nuclear and membrane labeling

* Add stub for weighted extraction in signal analysis

* Add a test for segmentation mask generation of just 2 cells

* Fix a colon issue in an if statement

* Change disk to circle for 0.16.2 (disk reqiures 0.17)

* Fix import of signal extraction

* Fix variable naming errors and out of scope issues

* Fix more library import stuff and variable naming issues

* Fix variable naming errors in segmentation mask generation

* Fix call to circle: takes separate x and y parameters rather than 1 tuple parameter

* Fix yet more variable naming errors (ugh...)

* Forgot to add a comma

* Fix (hopefully) the final variable naming error

* Fix tests up to membrane testing

* The segmentation mask tests with nuclear and membrane labeling should be good to go now

* Change dimensions so that indexing cell labels and hot spots is the first dimension

* Add first pass of synthetic_spatial_datagen with normal-based generation of nuclear and membrane channels

* Fix PEP8 and variable naming errors

* Fix function calls in synthetic_spatial_datagen_test

* Fix membrane_channel_data test: passed in wrong center

* Now I need to update border_2 from border_1 in same membrane_channel_data test...

* Now things should work after a membrane-based generation pat... (continued)

855 of 1077 relevant lines covered (79.39%)

0.79 hits per line

Jobs
ID Job ID Ran Files Coverage
1 938.1 (MPLBACKEND=Agg) 0
79.39
 Travis Job 938.1
Source Files on build 938
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