angelolab / segmentation / 506
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Synthetic data generation (Stage 1: distance-based) (#108)

* Initial commit of synthetic data branch

* Add function stubs for synthetic spatial generation functions

* Add generate_labels func definition

* Initial pass of synthetic data generation, will be working on a centroid-based version as well as testing functions

* Add a method to generate cluster centers, still need to check if they are within the parameter boundaries

* Replace tabs with spaces and fix more PEP8 violations

* Fix final PEP8 errors

* Rough draft of random centroid generation pushed

* Fix synthetic data generation in direct random initialization of matrix; forgot to account for a-a, b-b, b-c, c-c distances

* Finished debugging direct random matrix initialization; had to assure symmetry

* Fixed debugging point_init_dist_matrix; also had to ensure symmetry

* Fix PEP8 errors

* Add function stubs for testing of synthetic data generation functions

* Add some more comments and do a second pass

* Add initial tests to synthetic_spatial_datagen_test.py and transfer assertions in synthetic_spatial_datagen.py there

* Fix PEP8 errors and variable naming errors in testing function

* Add some more function fixes

* Fix function call to random point initialization

* Fix constants in synthetic_spatial_datagen.py to ensure AB > AC, and fix more PEP8 errors in corresponding test file

* Fix get_random_centroid_centers to transform into a label mat to be used by calc_distance_matrix

* Improve duplicate removal of generated points and return the resulting label matrix

* Remove point init dist matrix test function since direct_init_dist_matrix will be enough to test the results for that

* Fix PEP8 errors

* Fix indentation PEP8 errors

* Update point_init_dist_matrix to return a distance matrix as definted by Jay's function

* Remove leftover assertion statement from direct_init_dist_matrix

* Address Noah's concerns about the da... (continued)

634 of 893 relevant lines covered (71.0%)

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Jobs
ID Job ID Ran Files Coverage
1 506.1 (MPLBACKEND=Agg) 0
71.0
 Travis Job 506.1
Source Files on build 506
Detailed source file information is not available for this build.