Merge main to inference #35
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* added make_centered_bboxes & normalize_bboxes * added make_centered_bboxes & normalize_bboxes * created test_instance_cropping.py * added test normalize bboxes; added find_global_peaks_rough * black formatted * black formatted peak_finding * added make_grid_vectors, normalize_bboxes, integral_regression, added docstring to make_centered_bboxes, fixed find_global_peaks_rough; added crop_bboxes * finished find_global_peaks with integral regression over centroid crops! * reformatted with pydocstyle & black * moved make_grid_vectors to data/utils * removed normalize_bboxes * added tests docstrings * sorted imports with isort * remove unused imports * updated test cases for instance cropping * added minimal_cms.pt fixture + unit tests * added minimal_bboxes fixture; added unit tests for crop_bboxes & integral_regression * added find_global_peaks unit tests * finished find_local_peaks_rough! * finished find_local_peaks! * added unit tests for find_local_peaks and find_local_peaks_rough * updated test cases * added more test cases for find_local_peaks * updated test cases * added architectures folder * added maxpool2d same padding, get_act_fn; added simpleconvblock, simpleupsamplingblock, encoder, decoder; added unet * added test_unet_reference * black formatted common.py & test_unet.py * deleted tmp nb * _calc_same_pad returns int * fixed test case * added simpleconvblock tests * added tests * added tests for simple upsampling block * updated test_unet * removed unnecessary variables * updated augmentation random erase default values * created data/pipelines.py * added base config in config/data; temporary till config system settled * updated variable defaults to 0 and edited variable names in augmentation * updated parameter names in data/instance_cropping * added data/pipelines topdown pipeline make_base_pipeline * added test_pipelines * removed configs * updated augmentation class * modified test * removed cuda cache * added Model builder class and heads * added type hinting for init * black reformatted heads.py * updated model.py * updated test_model.py * updated test_model.py * updated pipelines docstring * added from_config for Model * added more act fn to get_act_fn * black reformatted & updated model.py & test_model.py * updated config, typehints, black formatted & added doc strings * added test_heads.py * updated module docstring * updated Model docstring * added coderabbit suggestions * black reformat * added 2 helper methods for getting backbone/head; separated common and utils in architectures * removed comments * updated test_get_act_fn * added multi-head feature to Model * black reformatted model.py * added all test cases for heads.py * reformatted test_heads.py * updated L44 in confidence_maps.py * added output channels to unet * resolved merge conflicts + small bugs * black reformatted * added coderabbit suggestions * not sure how intermediate features + multi head would work * Separate Augmentations into Intensity and Geometric (#18) * initial commit * separated intensity and geometric augmentations * test * pseudo code in model.py * small fix * name property in heads.py * name of head docstring added * added ruff cache to gitignore; added head selection in Model class * updated return value for decoder * small change to model.py * made model.py forward more efficient * small comments updated in instance_cropping for clarity * updated output structure of unet to dict; updated model.py attribute head * added single instance confmaps pipeline * added test cases * fixed batching issue * updated test cases * fixed pydocstyle * updated toml; added keep keys explicitly; added test case for singleinstance pipeline * updated toml * updated test_pipelines.py test case * black reformatted --------- Co-authored-by: Talmo Pereira <talmo@salk.edu>
modify keys
* find_global_peaks_rough_fix * lint fix * ruff lint fix * Format file --------- Co-authored-by: gitttt-1234 <64513125+gitttt-1234@users.noreply.github.com>
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## divya/inference #35 +/- ##
====================================================
- Coverage 99.78% 84.77% -15.02%
====================================================
Files 19 21 +2
Lines 936 1274 +338
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+ Hits 934 1080 +146
- Misses 2 194 +192 ☔ View full report in Codecov by Sentry. |
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