From 5387226c00c8194a2c18c13b0c1d75978ff1b8a5 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Thu, 18 Jan 2024 16:56:03 +0100
Subject: [PATCH] Rename package from ptbench -> mednet (closes #46)
---
.reuse/dep5 | 8 +-
MANIFEST.in | 2 +-
README.md | 8 +-
doc/api.rst | 56 ++--
doc/cli.rst | 6 +-
doc/conf.py | 2 +-
doc/config.rst | 104 +++----
doc/index.rst | 4 +-
doc/install.rst | 30 +-
doc/results/index.rst | 38 +--
doc/results/optimization/densenet.rst | 2 +-
doc/results/optimization/logreg.rst | 2 +-
doc/results/optimization/pasa.rst | 2 +-
doc/results/optimization/signstotb.rst | 2 +-
doc/results/runtime.rst | 2 +-
doc/usage/aggregpred.rst | 6 +-
doc/usage/evaluation.rst | 20 +-
doc/usage/index.rst | 12 +-
doc/usage/predtojson.rst | 6 +-
doc/usage/training.rst | 18 +-
pyproject.toml | 284 +++++++++---------
src/{ptbench => mednet}/__init__.py | 0
src/{ptbench => mednet}/config/__init__.py | 0
.../config/data/__init__.py | 0
.../config/data/hivtb/__init__.py | 0
.../config/data/hivtb/datamodule.py | 14 +-
.../config/data/hivtb/fold-0.json | 0
.../config/data/hivtb/fold-1.json | 0
.../config/data/hivtb/fold-2.json | 0
.../config/data/hivtb/fold-3.json | 0
.../config/data/hivtb/fold-4.json | 0
.../config/data/hivtb/fold-5.json | 0
.../config/data/hivtb/fold-6.json | 0
.../config/data/hivtb/fold-7.json | 0
.../config/data/hivtb/fold-8.json | 0
.../config/data/hivtb/fold-9.json | 0
.../config/data/hivtb/fold_0.py | 4 +-
.../config/data/hivtb/fold_1.py | 4 +-
.../config/data/hivtb/fold_2.py | 4 +-
.../config/data/hivtb/fold_3.py | 4 +-
.../config/data/hivtb/fold_4.py | 4 +-
.../config/data/hivtb/fold_5.py | 4 +-
.../config/data/hivtb/fold_6.py | 4 +-
.../config/data/hivtb/fold_7.py | 4 +-
.../config/data/hivtb/fold_8.py | 4 +-
.../config/data/hivtb/fold_9.py | 4 +-
.../config/data/indian/__init__.py | 0
.../config/data/indian/datamodule.py | 8 +-
.../config/data/indian/default.json | 0
.../config/data/indian/default.py | 4 +-
.../config/data/indian/fold-0.json | 0
.../config/data/indian/fold-1.json | 0
.../config/data/indian/fold-2.json | 0
.../config/data/indian/fold-3.json | 0
.../config/data/indian/fold-4.json | 0
.../config/data/indian/fold-5.json | 0
.../config/data/indian/fold-6.json | 0
.../config/data/indian/fold-7.json | 0
.../config/data/indian/fold-8.json | 0
.../config/data/indian/fold-9.json | 0
.../config/data/indian/fold_0.py | 4 +-
.../config/data/indian/fold_1.py | 4 +-
.../config/data/indian/fold_2.py | 4 +-
.../config/data/indian/fold_3.py | 4 +-
.../config/data/indian/fold_4.py | 4 +-
.../config/data/indian/fold_5.py | 4 +-
.../config/data/indian/fold_6.py | 4 +-
.../config/data/indian/fold_7.py | 4 +-
.../config/data/indian/fold_8.py | 4 +-
.../config/data/indian/fold_9.py | 4 +-
.../config/data/montgomery/__init__.py | 0
.../config/data/montgomery/datamodule.py | 14 +-
.../config/data/montgomery/default.json | 0
.../config/data/montgomery/default.py | 4 +-
.../config/data/montgomery/fold-0.json | 0
.../config/data/montgomery/fold-1.json | 0
.../config/data/montgomery/fold-2.json | 0
.../config/data/montgomery/fold-3.json | 0
.../config/data/montgomery/fold-4.json | 0
.../config/data/montgomery/fold-5.json | 0
.../config/data/montgomery/fold-6.json | 0
.../config/data/montgomery/fold-7.json | 0
.../config/data/montgomery/fold-8.json | 0
.../config/data/montgomery/fold-9.json | 0
.../config/data/montgomery/fold_0.py | 4 +-
.../config/data/montgomery/fold_1.py | 4 +-
.../config/data/montgomery/fold_2.py | 4 +-
.../config/data/montgomery/fold_3.py | 4 +-
.../config/data/montgomery/fold_4.py | 4 +-
.../config/data/montgomery/fold_5.py | 4 +-
.../config/data/montgomery/fold_6.py | 4 +-
.../config/data/montgomery/fold_7.py | 4 +-
.../config/data/montgomery/fold_8.py | 4 +-
.../config/data/montgomery/fold_9.py | 4 +-
.../data/montgomery_shenzhen/__init__.py | 0
.../data/montgomery_shenzhen/datamodule.py | 3 +-
.../data/montgomery_shenzhen/default.py | 2 +-
.../config/data/montgomery_shenzhen/fold_0.py | 2 +-
.../config/data/montgomery_shenzhen/fold_1.py | 2 +-
.../config/data/montgomery_shenzhen/fold_2.py | 2 +-
.../config/data/montgomery_shenzhen/fold_3.py | 2 +-
.../config/data/montgomery_shenzhen/fold_4.py | 2 +-
.../config/data/montgomery_shenzhen/fold_5.py | 2 +-
.../config/data/montgomery_shenzhen/fold_6.py | 2 +-
.../config/data/montgomery_shenzhen/fold_7.py | 2 +-
.../config/data/montgomery_shenzhen/fold_8.py | 2 +-
.../config/data/montgomery_shenzhen/fold_9.py | 2 +-
.../montgomery_shenzhen_indian/__init__.py | 0
.../montgomery_shenzhen_indian/datamodule.py | 24 +-
.../montgomery_shenzhen_indian/default.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_0.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_1.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_2.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_3.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_4.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_5.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_6.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_7.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_8.py | 2 +-
.../data/montgomery_shenzhen_indian/fold_9.py | 2 +-
.../__init__.py | 0
.../datamodule.py | 32 +-
.../default.py | 4 +-
.../__init__.py | 0
.../datamodule.py | 30 +-
.../v1_fold_0.py | 2 +-
.../v1_fold_1.py | 4 +-
.../v1_fold_2.py | 4 +-
.../v1_fold_3.py | 4 +-
.../v1_fold_4.py | 4 +-
.../v1_fold_5.py | 4 +-
.../v1_fold_6.py | 4 +-
.../v1_fold_7.py | 4 +-
.../v1_fold_8.py | 4 +-
.../v1_fold_9.py | 4 +-
.../v1_healthy_vs_atb.py | 4 +-
.../v2_fold_0.py | 4 +-
.../v2_fold_1.py | 4 +-
.../v2_fold_2.py | 4 +-
.../v2_fold_3.py | 4 +-
.../v2_fold_4.py | 4 +-
.../v2_fold_5.py | 4 +-
.../v2_fold_6.py | 4 +-
.../v2_fold_7.py | 4 +-
.../v2_fold_8.py | 4 +-
.../v2_fold_9.py | 4 +-
.../v2_others_vs_atb.py | 4 +-
.../config/data/nih_cxr14/__init__.py | 0
.../config/data/nih_cxr14/cardiomegaly.json | 0
.../config/data/nih_cxr14/cardiomegaly.py | 4 +-
.../config/data/nih_cxr14/datamodule.py | 12 +-
.../config/data/nih_cxr14/default.json.bz2 | Bin
.../config/data/nih_cxr14/default.py | 4 +-
.../data/nih_cxr14_padchest/__init__.py | 0
.../data/nih_cxr14_padchest/datamodule.py | 18 +-
.../config/data/nih_cxr14_padchest/idiap.py | 2 +-
.../config/data/padchest/__init__.py | 0
.../data/padchest/cardiomegaly-idiap.json | 0
.../data/padchest/cardiomegaly_idiap.py | 4 +-
.../config/data/padchest/datamodule.py | 14 +-
.../config/data/padchest/idiap.json.bz2 | Bin
.../config/data/padchest/idiap.py | 4 +-
.../config/data/padchest/no-tb-idiap.json.bz2 | Bin
.../config/data/padchest/no_tb_idiap.py | 4 +-
.../config/data/padchest/tb-idiap.json | 0
.../config/data/padchest/tb_idiap.py | 4 +-
.../config/data/shenzhen/__init__.py | 0
.../config/data/shenzhen/datamodule.py | 14 +-
.../config/data/shenzhen/default.json | 0
.../config/data/shenzhen/default.py | 4 +-
.../config/data/shenzhen/fold-0.json | 0
.../config/data/shenzhen/fold-1.json | 0
.../config/data/shenzhen/fold-2.json | 0
.../config/data/shenzhen/fold-3.json | 0
.../config/data/shenzhen/fold-4.json | 0
.../config/data/shenzhen/fold-5.json | 0
.../config/data/shenzhen/fold-6.json | 0
.../config/data/shenzhen/fold-7.json | 0
.../config/data/shenzhen/fold-8.json | 0
.../config/data/shenzhen/fold-9.json | 0
.../config/data/shenzhen/fold_0.py | 4 +-
.../config/data/shenzhen/fold_1.py | 4 +-
.../config/data/shenzhen/fold_2.py | 4 +-
.../config/data/shenzhen/fold_3.py | 4 +-
.../config/data/shenzhen/fold_4.py | 4 +-
.../config/data/shenzhen/fold_5.py | 4 +-
.../config/data/shenzhen/fold_6.py | 4 +-
.../config/data/shenzhen/fold_7.py | 4 +-
.../config/data/shenzhen/fold_8.py | 4 +-
.../config/data/shenzhen/fold_9.py | 4 +-
.../config/data/tbpoc/__init__.py | 0
.../config/data/tbpoc/datamodule.py | 14 +-
.../config/data/tbpoc/fold-0.json | 0
.../config/data/tbpoc/fold-1.json | 0
.../config/data/tbpoc/fold-2.json | 0
.../config/data/tbpoc/fold-3.json | 0
.../config/data/tbpoc/fold-4.json | 0
.../config/data/tbpoc/fold-5.json | 0
.../config/data/tbpoc/fold-6.json | 0
.../config/data/tbpoc/fold-7.json | 0
.../config/data/tbpoc/fold-8.json | 0
.../config/data/tbpoc/fold-9.json | 0
.../config/data/tbpoc/fold_0.py | 4 +-
.../config/data/tbpoc/fold_1.py | 4 +-
.../config/data/tbpoc/fold_2.py | 4 +-
.../config/data/tbpoc/fold_3.py | 4 +-
.../config/data/tbpoc/fold_4.py | 4 +-
.../config/data/tbpoc/fold_5.py | 4 +-
.../config/data/tbpoc/fold_6.py | 4 +-
.../config/data/tbpoc/fold_7.py | 4 +-
.../config/data/tbpoc/fold_8.py | 4 +-
.../config/data/tbpoc/fold_9.py | 4 +-
.../config/data/tbx11k/__init__.py | 0
.../config/data/tbx11k/datamodule.py | 12 +-
.../data/tbx11k/make_splits_from_database.py | 4 +-
.../config/data/tbx11k/v1-fold-0.json | 0
.../config/data/tbx11k/v1-fold-1.json | 0
.../config/data/tbx11k/v1-fold-2.json | 0
.../config/data/tbx11k/v1-fold-3.json | 0
.../config/data/tbx11k/v1-fold-4.json | 0
.../config/data/tbx11k/v1-fold-5.json | 0
.../config/data/tbx11k/v1-fold-6.json | 0
.../config/data/tbx11k/v1-fold-7.json | 0
.../config/data/tbx11k/v1-fold-8.json | 0
.../config/data/tbx11k/v1-fold-9.json | 0
.../config/data/tbx11k/v1-healthy-vs-atb.json | 0
.../config/data/tbx11k/v1_fold_0.py | 4 +-
.../config/data/tbx11k/v1_fold_1.py | 4 +-
.../config/data/tbx11k/v1_fold_2.py | 4 +-
.../config/data/tbx11k/v1_fold_3.py | 4 +-
.../config/data/tbx11k/v1_fold_4.py | 4 +-
.../config/data/tbx11k/v1_fold_5.py | 4 +-
.../config/data/tbx11k/v1_fold_6.py | 4 +-
.../config/data/tbx11k/v1_fold_7.py | 4 +-
.../config/data/tbx11k/v1_fold_8.py | 4 +-
.../config/data/tbx11k/v1_fold_9.py | 4 +-
.../config/data/tbx11k/v1_healthy_vs_atb.py | 4 +-
.../config/data/tbx11k/v2-fold-0.json | 0
.../config/data/tbx11k/v2-fold-1.json | 0
.../config/data/tbx11k/v2-fold-2.json | 0
.../config/data/tbx11k/v2-fold-3.json | 0
.../config/data/tbx11k/v2-fold-4.json | 0
.../config/data/tbx11k/v2-fold-5.json | 0
.../config/data/tbx11k/v2-fold-6.json | 0
.../config/data/tbx11k/v2-fold-7.json | 0
.../config/data/tbx11k/v2-fold-8.json | 0
.../config/data/tbx11k/v2-fold-9.json | 0
.../config/data/tbx11k/v2-others-vs-atb.json | 0
.../config/data/tbx11k/v2_fold_0.py | 4 +-
.../config/data/tbx11k/v2_fold_1.py | 4 +-
.../config/data/tbx11k/v2_fold_2.py | 4 +-
.../config/data/tbx11k/v2_fold_3.py | 4 +-
.../config/data/tbx11k/v2_fold_4.py | 4 +-
.../config/data/tbx11k/v2_fold_5.py | 4 +-
.../config/data/tbx11k/v2_fold_6.py | 4 +-
.../config/data/tbx11k/v2_fold_7.py | 4 +-
.../config/data/tbx11k/v2_fold_8.py | 4 +-
.../config/data/tbx11k/v2_fold_9.py | 4 +-
.../config/data/tbx11k/v2_others_vs_atb.py | 4 +-
.../config/models/__init__.py | 0
.../config/models/alexnet.py | 4 +-
.../config/models/alexnet_pretrained.py | 4 +-
.../config/models/densenet.py | 4 +-
.../config/models/densenet_pretrained.py | 4 +-
.../config/models/densenet_rs.py | 4 +-
.../config/models/logistic_regression.py | 2 +-
src/{ptbench => mednet}/config/models/mlp.py | 2 +-
src/{ptbench => mednet}/config/models/pasa.py | 4 +-
src/{ptbench => mednet}/data/__init__.py | 0
src/{ptbench => mednet}/data/augmentations.py | 0
src/{ptbench => mednet}/data/datamodule.py | 0
src/{ptbench => mednet}/data/image_utils.py | 0
src/{ptbench => mednet}/data/split.py | 0
src/{ptbench => mednet}/data/typing.py | 0
src/{ptbench => mednet}/engine/__init__.py | 0
src/{ptbench => mednet}/engine/callbacks.py | 0
src/{ptbench => mednet}/engine/device.py | 0
src/{ptbench => mednet}/engine/evaluator.py | 0
src/{ptbench => mednet}/engine/loggers.py | 0
src/{ptbench => mednet}/engine/predictor.py | 0
src/{ptbench => mednet}/engine/trainer.py | 0
src/{ptbench => mednet}/models/__init__.py | 0
src/{ptbench => mednet}/models/alexnet.py | 0
src/{ptbench => mednet}/models/densenet.py | 0
.../models/logistic_regression.py | 0
.../models/loss_weights.py | 0
src/{ptbench => mednet}/models/mlp.py | 0
src/{ptbench => mednet}/models/normalizer.py | 0
src/{ptbench => mednet}/models/pasa.py | 0
src/{ptbench => mednet}/models/separate.py | 0
src/{ptbench => mednet}/models/transforms.py | 0
src/{ptbench => mednet}/models/typing.py | 0
src/{ptbench => mednet}/scripts/__init__.py | 0
src/{ptbench => mednet}/scripts/cli.py | 0
src/{ptbench => mednet}/scripts/click.py | 0
src/{ptbench => mednet}/scripts/config.py | 18 +-
src/{ptbench => mednet}/scripts/database.py | 10 +-
src/{ptbench => mednet}/scripts/evaluate.py | 6 +-
src/{ptbench => mednet}/scripts/experiment.py | 4 +-
src/{ptbench => mednet}/scripts/predict.py | 6 +-
src/{ptbench => mednet}/scripts/train.py | 4 +-
.../scripts/train_analysis.py | 2 +-
src/{ptbench => mednet}/scripts/utils.py | 0
src/{ptbench => mednet}/utils/__init__.py | 0
src/{ptbench => mednet}/utils/checkpointer.py | 0
src/{ptbench => mednet}/utils/rc.py | 2 +-
src/{ptbench => mednet}/utils/resources.py | 0
src/{ptbench => mednet}/utils/summary.py | 0
src/{ptbench => mednet}/utils/tensorboard.py | 0
tests/conftest.py | 18 +-
tests/test_cli.py | 50 +--
tests/test_database_split.py | 2 +-
tests/test_evaluator.py | 2 +-
tests/test_hivtb.py | 4 +-
tests/test_image_utils.py | 2 +-
tests/test_indian.py | 4 +-
tests/test_montgomery.py | 4 +-
tests/test_montgomery_shenzhen.py | 10 +-
tests/test_montgomery_shenzhen_indian.py | 14 +-
...est_montgomery_shenzhen_indian_padchest.py | 18 +-
.../test_montgomery_shenzhen_indian_tbx11k.py | 18 +-
tests/test_nih_cxr14.py | 4 +-
tests/test_nih_cxr14_padchest.py | 10 +-
tests/test_padchest.py | 4 +-
tests/test_shenzhen.py | 4 +-
tests/test_summary.py | 4 +-
tests/test_tbpoc.py | 4 +-
tests/test_tbx11k.py | 4 +-
tests/test_tranforms.py | 2 +-
329 files changed, 774 insertions(+), 775 deletions(-)
rename src/{ptbench => mednet}/__init__.py (100%)
rename src/{ptbench => mednet}/config/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/hivtb/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/hivtb/datamodule.py (91%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-0.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-1.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-2.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-3.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-4.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-5.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-6.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-7.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-8.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold-9.json (100%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_0.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_1.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_2.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_3.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_4.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_5.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_6.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_7.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_8.py (65%)
rename src/{ptbench => mednet}/config/data/hivtb/fold_9.py (65%)
rename src/{ptbench => mednet}/config/data/indian/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/indian/datamodule.py (90%)
rename src/{ptbench => mednet}/config/data/indian/default.json (100%)
rename src/{ptbench => mednet}/config/data/indian/default.py (65%)
rename src/{ptbench => mednet}/config/data/indian/fold-0.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-1.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-2.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-3.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-4.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-5.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-6.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-7.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-8.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold-9.json (100%)
rename src/{ptbench => mednet}/config/data/indian/fold_0.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_1.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_2.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_3.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_4.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_5.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_6.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_7.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_8.py (66%)
rename src/{ptbench => mednet}/config/data/indian/fold_9.py (66%)
rename src/{ptbench => mednet}/config/data/montgomery/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/montgomery/datamodule.py (91%)
rename src/{ptbench => mednet}/config/data/montgomery/default.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/default.py (67%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-0.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-1.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-2.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-3.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-4.json (100%)
rename src/{ptbench => mednet}/config/data/montgomery/fold-5.json (100%)
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rename src/{ptbench => mednet}/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py (82%)
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rename src/{ptbench => mednet}/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py (82%)
rename src/{ptbench => mednet}/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py (83%)
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rename src/{ptbench => mednet}/config/data/nih_cxr14_padchest/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/nih_cxr14_padchest/datamodule.py (73%)
rename src/{ptbench => mednet}/config/data/nih_cxr14_padchest/idiap.py (81%)
rename src/{ptbench => mednet}/config/data/padchest/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/padchest/cardiomegaly-idiap.json (100%)
rename src/{ptbench => mednet}/config/data/padchest/cardiomegaly_idiap.py (77%)
rename src/{ptbench => mednet}/config/data/padchest/datamodule.py (96%)
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rename src/{ptbench => mednet}/config/data/padchest/idiap.py (77%)
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rename src/{ptbench => mednet}/config/data/padchest/no_tb_idiap.py (83%)
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rename src/{ptbench => mednet}/config/data/padchest/tb_idiap.py (80%)
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rename src/{ptbench => mednet}/config/data/shenzhen/fold_0.py (70%)
rename src/{ptbench => mednet}/config/data/shenzhen/fold_1.py (70%)
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rename src/{ptbench => mednet}/config/data/tbpoc/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/datamodule.py (91%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-0.json (100%)
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rename src/{ptbench => mednet}/config/data/tbpoc/fold-4.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-5.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-6.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-7.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-8.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold-9.json (100%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_0.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_1.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_2.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_3.py (67%)
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rename src/{ptbench => mednet}/config/data/tbpoc/fold_5.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_6.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_7.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_8.py (67%)
rename src/{ptbench => mednet}/config/data/tbpoc/fold_9.py (67%)
rename src/{ptbench => mednet}/config/data/tbx11k/__init__.py (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/datamodule.py (96%)
rename src/{ptbench => mednet}/config/data/tbx11k/make_splits_from_database.py (99%)
rename src/{ptbench => mednet}/config/data/tbx11k/v1-fold-0.json (100%)
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rename src/{ptbench => mednet}/config/data/tbx11k/v1_fold_0.py (69%)
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rename src/{ptbench => mednet}/config/data/tbx11k/v1_fold_6.py (69%)
rename src/{ptbench => mednet}/config/data/tbx11k/v1_fold_7.py (69%)
rename src/{ptbench => mednet}/config/data/tbx11k/v1_fold_8.py (69%)
rename src/{ptbench => mednet}/config/data/tbx11k/v1_fold_9.py (69%)
rename src/{ptbench => mednet}/config/data/tbx11k/v1_healthy_vs_atb.py (82%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2-fold-0.json (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2-fold-1.json (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2-fold-2.json (100%)
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rename src/{ptbench => mednet}/config/data/tbx11k/v2-fold-8.json (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2-fold-9.json (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2-others-vs-atb.json (100%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_0.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_1.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_2.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_3.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_4.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_5.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_6.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_7.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_8.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_fold_9.py (70%)
rename src/{ptbench => mednet}/config/data/tbx11k/v2_others_vs_atb.py (84%)
rename src/{ptbench => mednet}/config/models/__init__.py (100%)
rename src/{ptbench => mednet}/config/models/alexnet.py (86%)
rename src/{ptbench => mednet}/config/models/alexnet_pretrained.py (87%)
rename src/{ptbench => mednet}/config/models/densenet.py (86%)
rename src/{ptbench => mednet}/config/models/densenet_pretrained.py (87%)
rename src/{ptbench => mednet}/config/models/densenet_rs.py (88%)
rename src/{ptbench => mednet}/config/models/logistic_regression.py (86%)
rename src/{ptbench => mednet}/config/models/mlp.py (87%)
rename src/{ptbench => mednet}/config/models/pasa.py (88%)
rename src/{ptbench => mednet}/data/__init__.py (100%)
rename src/{ptbench => mednet}/data/augmentations.py (100%)
rename src/{ptbench => mednet}/data/datamodule.py (100%)
rename src/{ptbench => mednet}/data/image_utils.py (100%)
rename src/{ptbench => mednet}/data/split.py (100%)
rename src/{ptbench => mednet}/data/typing.py (100%)
rename src/{ptbench => mednet}/engine/__init__.py (100%)
rename src/{ptbench => mednet}/engine/callbacks.py (100%)
rename src/{ptbench => mednet}/engine/device.py (100%)
rename src/{ptbench => mednet}/engine/evaluator.py (100%)
rename src/{ptbench => mednet}/engine/loggers.py (100%)
rename src/{ptbench => mednet}/engine/predictor.py (100%)
rename src/{ptbench => mednet}/engine/trainer.py (100%)
rename src/{ptbench => mednet}/models/__init__.py (100%)
rename src/{ptbench => mednet}/models/alexnet.py (100%)
rename src/{ptbench => mednet}/models/densenet.py (100%)
rename src/{ptbench => mednet}/models/logistic_regression.py (100%)
rename src/{ptbench => mednet}/models/loss_weights.py (100%)
rename src/{ptbench => mednet}/models/mlp.py (100%)
rename src/{ptbench => mednet}/models/normalizer.py (100%)
rename src/{ptbench => mednet}/models/pasa.py (100%)
rename src/{ptbench => mednet}/models/separate.py (100%)
rename src/{ptbench => mednet}/models/transforms.py (100%)
rename src/{ptbench => mednet}/models/typing.py (100%)
rename src/{ptbench => mednet}/scripts/__init__.py (100%)
rename src/{ptbench => mednet}/scripts/cli.py (100%)
rename src/{ptbench => mednet}/scripts/click.py (100%)
rename src/{ptbench => mednet}/scripts/config.py (92%)
rename src/{ptbench => mednet}/scripts/database.py (95%)
rename src/{ptbench => mednet}/scripts/evaluate.py (95%)
rename src/{ptbench => mednet}/scripts/experiment.py (97%)
rename src/{ptbench => mednet}/scripts/predict.py (94%)
rename src/{ptbench => mednet}/scripts/train.py (99%)
rename src/{ptbench => mednet}/scripts/train_analysis.py (98%)
rename src/{ptbench => mednet}/scripts/utils.py (100%)
rename src/{ptbench => mednet}/utils/__init__.py (100%)
rename src/{ptbench => mednet}/utils/checkpointer.py (100%)
rename src/{ptbench => mednet}/utils/rc.py (86%)
rename src/{ptbench => mednet}/utils/resources.py (100%)
rename src/{ptbench => mednet}/utils/summary.py (100%)
rename src/{ptbench => mednet}/utils/tensorboard.py (100%)
diff --git a/.reuse/dep5 b/.reuse/dep5
index 4e2a69c2..9ddad99c 100644
--- a/.reuse/dep5
+++ b/.reuse/dep5
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: ptbench
+Upstream-Name: mednet
Upstream-Contact: Andre Anjos <andre.anjos@idiap.ch>
-Source: https://gitlab.idiap.ch/biosignal/software/ptbench
+Source: https://gitlab.idiap.ch/biosignal/software/mednet
Files:
.gitmodules
@@ -15,8 +15,8 @@ Files:
doc/results/img/*.jpg
doc/results/img/*.png
doc/results/img/*/*.jpg
- src/ptbench/config/data/*/*.json
- src/ptbench/config/data/*/*.json.bz2
+ src/mednet/config/data/*/*.json
+ src/mednet/config/data/*/*.json.bz2
tests/data/*.csv
tests/data/*.json
tests/data/*.png
diff --git a/MANIFEST.in b/MANIFEST.in
index 2d400b18..5b589c03 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -4,4 +4,4 @@
recursive-include doc *.rst *.png
recursive-include tests *.py *.png *.csv *.json
-recursive-include src/ptbench/config/data *.json *.json.bz2
+recursive-include src/mednet/config/data *.json *.json.bz2
diff --git a/README.md b/README.md
index 810b740d..12c83b13 100644
--- a/README.md
+++ b/README.md
@@ -3,10 +3,10 @@ SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idia
SPDX-License-Identifier: GPL-3.0-or-later
-->
-[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/ptbench/main/sphinx/index.html)
-[](https://gitlab.idiap.ch/biosignal/software/ptbench/commits/main)
-[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/ptbench/main/coverage/index.html)
-[](https://gitlab.idiap.ch/biosignal/software/ptbench)
+[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/mednet/main/sphinx/index.html)
+[](https://gitlab.idiap.ch/biosignal/software/mednet/commits/main)
+[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/mednet/main/coverage/index.html)
+[](https://gitlab.idiap.ch/biosignal/software/mednet)
# Computer-Aided Disease Detection from Medical Data
diff --git a/doc/api.rst b/doc/api.rst
index e166ddbe..bba77bc5 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -2,17 +2,17 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.api:
+.. _mednet.api:
============
Python API
============
This section includes information for using the Python API of
-``ptbench``.
+``mednet``.
-.. _ptbench.api.data:
+.. _mednet.api.data:
Data Methods
------------
@@ -22,14 +22,14 @@ Auxiliary classes and methods to define raw dataset iterators.
.. autosummary::
:toctree: api/data
- ptbench.data.augmentations
- ptbench.data.datamodule
- ptbench.data.image_utils
- ptbench.data.split
- ptbench.data.typing
+ mednet.data.augmentations
+ mednet.data.datamodule
+ mednet.data.image_utils
+ mednet.data.split
+ mednet.data.typing
-.. _ptbench.api.models:
+.. _mednet.api.models:
Models
------
@@ -39,16 +39,16 @@ CNN and other models implemented.
.. autosummary::
:toctree: api/models
- ptbench.models.pasa
- ptbench.models.alexnet
- ptbench.models.densenet
- ptbench.models.normalizer
- ptbench.models.logistic_regression
- ptbench.models.mlp
- ptbench.models.typing
+ mednet.models.pasa
+ mednet.models.alexnet
+ mednet.models.densenet
+ mednet.models.normalizer
+ mednet.models.logistic_regression
+ mednet.models.mlp
+ mednet.models.typing
-.. _ptbench.api.engines:
+.. _mednet.api.engines:
Command engines
---------------
@@ -58,15 +58,15 @@ Functions to actuate on the data.
.. autosummary::
:toctree: api/engine
- ptbench.engine.device
- ptbench.engine.callbacks
- ptbench.engine.trainer
- ptbench.engine.predictor
- ptbench.engine.evaluator
+ mednet.engine.device
+ mednet.engine.callbacks
+ mednet.engine.trainer
+ mednet.engine.predictor
+ mednet.engine.evaluator
-.. _ptbench.api.utils:
+.. _mednet.api.utils:
Various utilities
-----------------
@@ -76,11 +76,11 @@ Reusable auxiliary functions.
.. autosummary::
:toctree: api/utils
- ptbench.utils.checkpointer
- ptbench.utils.rc
- ptbench.utils.resources
- ptbench.utils.summary
- ptbench.utils.tensorboard
+ mednet.utils.checkpointer
+ mednet.utils.rc
+ mednet.utils.resources
+ mednet.utils.summary
+ mednet.utils.tensorboard
.. include:: links.rst
diff --git a/doc/cli.rst b/doc/cli.rst
index 950e3cdc..0d9ebcec 100644
--- a/doc/cli.rst
+++ b/doc/cli.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.cli:
+.. _mednet.cli:
========================
Command-line Interface
@@ -12,8 +12,8 @@ This section contains an overview of command-line applications shipped with
this package.
-.. click:: ptbench.scripts.cli:cli
- :prog: ptbench
+.. click:: mednet.scripts.cli:cli
+ :prog: mednet
:nested: full
diff --git a/doc/conf.py b/doc/conf.py
index e9d570d2..1411e92d 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -68,7 +68,7 @@ source_suffix = ".rst"
main_doc = "index"
# General information about the project.
-project = "ptbench"
+project = "mednet"
package = distribution(project)
copyright = "%s, Idiap Research Institute" % time.strftime("%Y")
diff --git a/doc/config.rst b/doc/config.rst
index 93c4559a..1d6c5af9 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.config:
+.. _mednet.config:
Preset Configurations
---------------------
@@ -11,7 +11,7 @@ This module contains preset configurations for baseline CNN architectures and
datamodules.
-.. _ptbench.config.models:
+.. _mednet.config.models:
Pre-configured Models
=====================
@@ -22,17 +22,17 @@ Pre-configured models you can readily use.
:toctree: api/config.models
:template: config.rst
- ptbench.config.models.alexnet
- ptbench.config.models.alexnet_pretrained
- ptbench.config.models.densenet
- ptbench.config.models.densenet_pretrained
- ptbench.config.models.densenet_rs
- ptbench.config.models.logistic_regression
- ptbench.config.models.mlp
- ptbench.config.models.pasa
+ mednet.config.models.alexnet
+ mednet.config.models.alexnet_pretrained
+ mednet.config.models.densenet
+ mednet.config.models.densenet_pretrained
+ mednet.config.models.densenet_rs
+ mednet.config.models.logistic_regression
+ mednet.config.models.mlp
+ mednet.config.models.pasa
-.. _ptbench.config.datamodules:
+.. _mednet.config.datamodules:
DataModule support
==================
@@ -45,22 +45,22 @@ functional data module that can be used in training, prediction or testing.
.. autosummary::
:toctree: api/config.datamodules
- ptbench.config.data.hivtb.datamodule
- ptbench.config.data.indian.datamodule
- ptbench.config.data.montgomery.datamodule
- ptbench.config.data.montgomery_shenzhen.datamodule
- ptbench.config.data.montgomery_shenzhen_indian.datamodule
- ptbench.config.data.montgomery_shenzhen_indian_padchest.datamodule
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.datamodule
- ptbench.config.data.nih_cxr14.datamodule
- ptbench.config.data.nih_cxr14_padchest.datamodule
- ptbench.config.data.padchest.datamodule
- ptbench.config.data.shenzhen.datamodule
- ptbench.config.data.tbpoc.datamodule
- ptbench.config.data.tbx11k.datamodule
+ mednet.config.data.hivtb.datamodule
+ mednet.config.data.indian.datamodule
+ mednet.config.data.montgomery.datamodule
+ mednet.config.data.montgomery_shenzhen.datamodule
+ mednet.config.data.montgomery_shenzhen_indian.datamodule
+ mednet.config.data.montgomery_shenzhen_indian_padchest.datamodule
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.datamodule
+ mednet.config.data.nih_cxr14.datamodule
+ mednet.config.data.nih_cxr14_padchest.datamodule
+ mednet.config.data.padchest.datamodule
+ mednet.config.data.shenzhen.datamodule
+ mednet.config.data.tbpoc.datamodule
+ mednet.config.data.tbx11k.datamodule
-.. _ptbench.config.datamodule-instances:
+.. _mednet.config.datamodule-instances:
Pre-configured DataModules
==========================
@@ -68,29 +68,29 @@ Pre-configured DataModules
DataModules provide access to preset pytorch dataloaders for training,
validating, testing and running prediction tasks. Each of the pre-configured
DataModule is based on one (or more) of the :ref:`supported base data modules
-<ptbench.config.datamodules>`.
+<mednet.config.datamodules>`.
.. autosummary::
:toctree: api/config.datamodule-instances
:template: config.rst
- ptbench.config.data.indian.default
- ptbench.config.data.montgomery.default
- ptbench.config.data.montgomery_shenzhen.default
- ptbench.config.data.montgomery_shenzhen_indian.default
- ptbench.config.data.montgomery_shenzhen_indian_padchest.default
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
- ptbench.config.data.nih_cxr14.default
- ptbench.config.data.nih_cxr14_padchest.idiap
- ptbench.config.data.padchest.idiap
- ptbench.config.data.shenzhen.default
- ptbench.config.data.tbx11k.v1_healthy_vs_atb
- ptbench.config.data.tbx11k.v2_others_vs_atb
- ptbench.config.data.tbx11k.v2_others_vs_atb
+ mednet.config.data.indian.default
+ mednet.config.data.montgomery.default
+ mednet.config.data.montgomery_shenzhen.default
+ mednet.config.data.montgomery_shenzhen_indian.default
+ mednet.config.data.montgomery_shenzhen_indian_padchest.default
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
+ mednet.config.data.nih_cxr14.default
+ mednet.config.data.nih_cxr14_padchest.idiap
+ mednet.config.data.padchest.idiap
+ mednet.config.data.shenzhen.default
+ mednet.config.data.tbx11k.v1_healthy_vs_atb
+ mednet.config.data.tbx11k.v2_others_vs_atb
+ mednet.config.data.tbx11k.v2_others_vs_atb
-.. _ptbench.config.datamodule-instances.folds:
+.. _mednet.config.datamodule-instances.folds:
Cross-validation DataModules
============================
@@ -105,17 +105,17 @@ datamodules. Nine other folds are available for every configuration (from 1 to
:toctree: api/config.datamodule-folds
:template: config.rst
- ptbench.config.data.hivtb.fold_0
- ptbench.config.data.indian.fold_0
- ptbench.config.data.montgomery.fold_0
- ptbench.config.data.montgomery_shenzhen.fold_0
- ptbench.config.data.montgomery_shenzhen_indian.fold_0
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
- ptbench.config.data.shenzhen.fold_0
- ptbench.config.data.tbpoc.fold_0
- ptbench.config.data.tbx11k.v1_fold_0
- ptbench.config.data.tbx11k.v2_fold_0
+ mednet.config.data.hivtb.fold_0
+ mednet.config.data.indian.fold_0
+ mednet.config.data.montgomery.fold_0
+ mednet.config.data.montgomery_shenzhen.fold_0
+ mednet.config.data.montgomery_shenzhen_indian.fold_0
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
+ mednet.config.data.shenzhen.fold_0
+ mednet.config.data.tbpoc.fold_0
+ mednet.config.data.tbx11k.v1_fold_0
+ mednet.config.data.tbx11k.v2_fold_0
.. include:: links.rst
diff --git a/doc/index.rst b/doc/index.rst
index e948754e..b0126ac0 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench:
+.. _mednet:
====================================================
Computer-Aided Disease Detection from Medical Data
@@ -38,7 +38,7 @@ Please use the BibTeX reference below to cite this work:
number = {Idiap-Com-01-2021},
year = {2021},
institution = {Idiap},
- url = {https://gitlab.idiap.ch/biosignal/software/ptbench},
+ url = {https://gitlab.idiap.ch/biosignal/software/mednet},
pdf = {https://publidiap.idiap.ch/downloads/reports/2021/Raposo_Idiap-Com-01-2021.pdf}
}
diff --git a/doc/install.rst b/doc/install.rst
index 7826c804..5b9e9098 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.install:
+.. _mednet.install:
==============
Installation
@@ -17,13 +17,13 @@ We support two installation modes, through pip_, or mamba_ (conda).
.. code:: sh
- pip install ptbench
+ pip install mednet
Latest beta, from GitLab package registry:
.. code:: sh
- pip install --pre --index-url https://gitlab.idiap.ch/api/v4/groups/software/-/packages/pypi/simple --extra-index-url https://pypi.org/simple ptbench
+ pip install --pre --index-url https://gitlab.idiap.ch/api/v4/groups/software/-/packages/pypi/simple --extra-index-url https://pypi.org/simple mednet
.. tip::
@@ -37,16 +37,16 @@ We support two installation modes, through pip_, or mamba_ (conda).
.. code:: sh
- mamba install -c https://www.idiap.ch/software/biosignal/conda -c conda-forge ptbench
+ mamba install -c https://www.idiap.ch/software/biosignal/conda -c conda-forge mednet
Latest beta:
.. code:: sh
- mamba install -c https://www.idiap.ch/software/biosignal/conda/label/beta -c conda-forge ptbench
+ mamba install -c https://www.idiap.ch/software/biosignal/conda/label/beta -c conda-forge mednet
-.. _ptbench.setup:
+.. _mednet.setup:
Setup
-----
@@ -54,7 +54,7 @@ Setup
A configuration file may be useful to setup global options that should be often
reused. The location of the configuration file depends on the value of the
environment variable ``$XDG_CONFIG_HOME``, but defaults to
-``~/.config/ptbench.toml``. You may edit this file using your preferred
+``~/.config/mednet.toml``. You may edit this file using your preferred
editor.
Here is an example configuration file that may be useful as a starting point:
@@ -78,7 +78,7 @@ Here is an example configuration file that may be useful as a starting point:
.. code:: sh
- ptbench dataset list
+ mednet dataset list
You must procure and download datasets by yourself. The raw data is not
@@ -89,10 +89,10 @@ Here is an example configuration file that may be useful as a starting point:
.. code:: sh
- ptbench dataset check montgomery
+ mednet dataset check montgomery
-.. _ptbench.setup.databases:
+.. _mednet.setup.databases:
Supported Databases
===================
@@ -103,7 +103,7 @@ raw data can be downloaded. The list of images in each split is available
in the source code.
-.. _ptbench.setup.databases.tb:
+.. _mednet.setup.databases.tb:
Tuberculosis databases
~~~~~~~~~~~~~~~~~~~~~~
@@ -144,7 +144,7 @@ In addition to the splits presented in the following table, 10 folds
- 52
-.. _ptbench.setup.datasets.tb+signs:
+.. _mednet.setup.datasets.tb+signs:
Tuberculosis multilabel databases
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -180,7 +180,7 @@ In addition to the splits presented in the following table, 10 folds
- 2800
-.. _ptbench.setup.datasets.tbmultilabel+signs:
+.. _mednet.setup.datasets.tbmultilabel+signs:
Tuberculosis + radiological findings dataset
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -204,7 +204,7 @@ and radiological findings.
- 0
-.. _ptbench.setup.datasets.signs:
+.. _mednet.setup.datasets.signs:
Radiological findings datasets
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -235,7 +235,7 @@ information about tuberculosis.
- 4'054
-.. _ptbench.setup.datasets.hiv-tb:
+.. _mednet.setup.datasets.hiv-tb:
HIV-Tuberculosis datasets
~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/results/index.rst b/doc/results/index.rst
index 0585e912..1fec86c3 100644
--- a/doc/results/index.rst
+++ b/doc/results/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results:
+.. _mednet.results:
=========
Results
@@ -59,9 +59,9 @@ Stratified k-folding has been used (10 folds) to generate these results.
.. tip::
To generate the following results, you first need to predict TB on each
- fold, then use the :ref:`aggregpred command <ptbench.cli>` to aggregate the
+ fold, then use the :ref:`aggregpred command <mednet.cli>` to aggregate the
predictions together, and finally evaluate this new file using the
- :ref:`compare command <ptbench.cli>`.
+ :ref:`compare command <mednet.cli>`.
Pasa and DenseNet-121 (random initialization)
"""""""""""""""""""""""""""""""""""""""""""""
@@ -113,37 +113,37 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC
- .. figure:: img/compare_pasa_mc_ch_kfold_500.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC-CH
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH
- .. figure:: img/compare_pasa_mc_ch_in_kfold_500.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC-CH-IN
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH-IN
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH-IN
* - .. figure:: img/compare_densenet_mc_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC
- .. figure:: img/compare_densenet_mc_ch_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH
- .. figure:: img/compare_densenet_mc_ch_in_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN
DenseNet-121 (pretrained on ImageNet)
"""""""""""""""""""""""""""""""""""""
@@ -180,19 +180,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC
- .. figure:: img/compare_densenetpreIN_mc_ch_kfold_600.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH
- .. figure:: img/compare_densenetpreIN_mc_ch_ch_kfold_600.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH-IN
Logistic Regression Classifier
""""""""""""""""""""""""""""""
@@ -229,19 +229,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC
- .. figure:: img/compare_logreg_mc_ch_kfold_100.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC-CH
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH
- .. figure:: img/compare_logreg_mc_ch_in_kfold_100.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC-CH-IN
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH-IN
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH-IN
DenseNet-121 (pretrained on ImageNet and NIH CXR14)
"""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -278,19 +278,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC (pretrained on NIH)
- .. figure:: img/compare_densenetpre_mc_ch_kfold_300.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH (pretrained on NIH)
- .. figure:: img/compare_densenetpre_mc_ch_in_kfold_300.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN (pretrained on NIH)
Global sensitivity analysis (relevance)
@@ -301,7 +301,7 @@ Model used to generate the following figures: LogReg trained on MC-CH-IN fold 0
.. tip::
Use the ``--relevance-analysis`` argument of the :ref:`predict command
- <ptbench.cli>` to generate the following plots.
+ <mednet.cli>` to generate the following plots.
* Green color: likely TB
* Orange color: Could be TB
diff --git a/doc/results/optimization/densenet.rst b/doc/results/optimization/densenet.rst
index d6a4c1a8..49bc27fe 100644
--- a/doc/results/optimization/densenet.rst
+++ b/doc/results/optimization/densenet.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.densenet:
+.. _mednet.results.optimization.densenet:
=============================
Densenet model optimization
diff --git a/doc/results/optimization/logreg.rst b/doc/results/optimization/logreg.rst
index cc8f8574..e988a524 100644
--- a/doc/results/optimization/logreg.rst
+++ b/doc/results/optimization/logreg.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.logreg:
+.. _mednet.results.optimization.logreg:
===========================
LogReg model optimization
diff --git a/doc/results/optimization/pasa.rst b/doc/results/optimization/pasa.rst
index 901d99f6..5c86dc88 100644
--- a/doc/results/optimization/pasa.rst
+++ b/doc/results/optimization/pasa.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.pasa:
+.. _mednet.results.optimization.pasa:
=========================
Pasa model optimization
diff --git a/doc/results/optimization/signstotb.rst b/doc/results/optimization/signstotb.rst
index a7b10034..52f06a17 100644
--- a/doc/results/optimization/signstotb.rst
+++ b/doc/results/optimization/signstotb.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.signstotb:
+.. _mednet.results.optimization.signstotb:
==============================
SignsToTB model optimization
diff --git a/doc/results/runtime.rst b/doc/results/runtime.rst
index 7f079c95..5f1737b5 100644
--- a/doc/results/runtime.rst
+++ b/doc/results/runtime.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.runtime:
+.. _mednet.results.runtime:
==============================================
Models training runtime and memory footprint
diff --git a/doc/usage/aggregpred.rst b/doc/usage/aggregpred.rst
index bcec1eef..661750bd 100644
--- a/doc/usage/aggregpred.rst
+++ b/doc/usage/aggregpred.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.aggregpred:
+.. _mednet.usage.aggregpred:
=======================================================
Aggregate multiple prediction files into a single one
@@ -13,12 +13,12 @@ one. It can be used when doing cross-validation to aggregate the predictions of
k different models before evaluating the aggregated predictions. We input
multiple prediction files (CSV files) and output a single one.
-Use the sub-command :ref:`aggregpred <ptbench.cli>` aggregate your prediction
+Use the sub-command :ref:`aggregpred <mednet.cli>` aggregate your prediction
files together:
.. code:: sh
- ptbench aggregpred -vv path/to/fold0/predictions.csv path/to/fold1/predictions.csv --output-folder=aggregpred
+ mednet aggregpred -vv path/to/fold0/predictions.csv path/to/fold1/predictions.csv --output-folder=aggregpred
.. include:: ../links.rst
diff --git a/doc/usage/evaluation.rst b/doc/usage/evaluation.rst
index 1778e126..d490f991 100644
--- a/doc/usage/evaluation.rst
+++ b/doc/usage/evaluation.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.evaluation:
+.. _mednet.usage.evaluation:
==========================
Inference and Evaluation
@@ -20,22 +20,22 @@ Inference
In inference (or prediction) mode, we input data, the trained model, and output
a CSV file containing the prediction outputs for every input image.
-To run inference, use the sub-command :ref:`predict <ptbench.cli>` to run
+To run inference, use the sub-command :ref:`predict <mednet.cli>` to run
prediction on an existing dataset:
.. code:: sh
- ptbench predict -vv <model> -w <path/to/model.pth> <dataset>
+ mednet predict -vv <model> -w <path/to/model.pth> <dataset>
Replace ``<model>`` and ``<dataset>`` by the appropriate :ref:`configuration
-files <ptbench.config>`. Replace ``<path/to/model.pth>`` to a path leading to
+files <mednet.config>`. Replace ``<path/to/model.pth>`` to a path leading to
the pre-trained model.
.. tip::
An option to generate grad-CAMs is available for the :py:mod:`DensenetRS
- <ptbench.config.models.densenet_rs>` model. To activate it, use the
+ <mednet.config.models.densenet_rs>` model. To activate it, use the
``--grad-cams`` argument.
.. tip::
@@ -49,29 +49,29 @@ Evaluation
In evaluation, we input a dataset and predictions to generate performance
summaries that help analysis of a trained model. Evaluation is done using the
-:ref:`evaluate command <ptbench.cli>` followed by the model and the annotated
+:ref:`evaluate command <mednet.cli>` followed by the model and the annotated
dataset configuration, and the path to the pretrained weights via the
``--weight`` argument.
-Use ``ptbench evaluate --help`` for more information.
+Use ``mednet evaluate --help`` for more information.
E.g. run evaluation on predictions from the Montgomery set, do the following:
.. code:: sh
- ptbench evaluate -vv montgomery -p /predictions/folder -o /eval/results/folder
+ mednet evaluate -vv montgomery -p /predictions/folder -o /eval/results/folder
Comparing Systems
-----------------
To compare multiple systems together and generate combined plots and tables,
-use the :ref:`compare command <ptbench.cli>`. Use ``--help`` for a quick
+use the :ref:`compare command <mednet.cli>`. Use ``--help`` for a quick
guide.
.. code:: sh
- ptbench compare -vv A A/metrics.csv B B/metrics.csv --output-figure=plot.pdf --output-table=table.txt --threshold=0.5
+ mednet compare -vv A A/metrics.csv B B/metrics.csv --output-figure=plot.pdf --output-table=table.txt --threshold=0.5
.. include:: ../links.rst
diff --git a/doc/usage/index.rst b/doc/usage/index.rst
index 34316bab..05dd6918 100644
--- a/doc/usage/index.rst
+++ b/doc/usage/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage:
+.. _mednet.usage:
=======
Usage
@@ -14,7 +14,7 @@ tuberculosis detection with support for the following activities.
.. figure:: img/direct_vs_indirect.png
-.. _ptbench.usage.direct-detection:
+.. _mednet.usage.direct-detection:
Direct detection
----------------
@@ -31,7 +31,7 @@ Direct detection
systems.
-.. _ptbench.usage.indirect-detection:
+.. _mednet.usage.indirect-detection:
Indirect detection
------------------
@@ -52,7 +52,7 @@ Indirect detection
* Comparison: Use predictions results to compare performance of multiple
systems.
-We provide :ref:`command-line interfaces (CLI) <ptbench.cli>` that implement
+We provide :ref:`command-line interfaces (CLI) <mednet.cli>` that implement
each of the phases above. This interface is configurable using :ref:`clapper's
extensible configuration framework <clapper.config>`. In essence, each
command-line option may be provided as a variable with the same name in a
@@ -67,14 +67,14 @@ to an application.
may require complex Python types that cannot be synthetized in a single
input parameter.
-We provide a number of :ref:`preset configuration files <ptbench.config>` that
+We provide a number of :ref:`preset configuration files <mednet.config>` that
can be used in one or more of the activities described in this section. Our
command-line framework allows you to refer to these preset configuration files
using special names (a.k.a. "resources"), that procure and load these for you
automatically.
-.. _ptbench.usage.commands:
+.. _mednet.usage.commands:
Commands
--------
diff --git a/doc/usage/predtojson.rst b/doc/usage/predtojson.rst
index 81e31d2f..30ff645a 100644
--- a/doc/usage/predtojson.rst
+++ b/doc/usage/predtojson.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.predtojson:
+.. _mednet.usage.predtojson:
========================================
Converting predictions to JSON dataset
@@ -13,12 +13,12 @@ into a JSON dataset. It can be used to create new versions of TB datasets with
the predicted radiological signs to be able to use a shallow model. We input
predictions (CSV files) and output a ``dataset.json`` file.
-Use the sub-command :ref:`predtojson <ptbench.cli>` to create your JSON dataset
+Use the sub-command :ref:`predtojson <mednet.cli>` to create your JSON dataset
file:
.. code:: sh
- ptbench predtojson -vv train train/predictions.csv test test/predictions.csv --output-folder=pred_to_json
+ mednet predtojson -vv train train/predictions.csv test test/predictions.csv --output-folder=pred_to_json
.. include:: ../links.rst
diff --git a/doc/usage/training.rst b/doc/usage/training.rst
index 5eb974cc..4172732e 100644
--- a/doc/usage/training.rst
+++ b/doc/usage/training.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.training:
+.. _mednet.usage.training:
==========
Training
@@ -11,10 +11,10 @@
Convolutional Neural Network (CNN)
----------------------------------
-To train a new CNN, use the command-line interface (CLI) application ``ptbench
+To train a new CNN, use the command-line interface (CLI) application ``mednet
train``, available on your prompt. To use this CLI, you must define the input
dataset that will be used to train the CNN, as well as the type of model that
-will be trained. You may issue ``ptbench train --help`` for a help message
+will be trained. You may issue ``mednet train --help`` for a help message
containing more detailed instructions.
.. tip::
@@ -31,23 +31,23 @@ To train Pasa CNN on the Montgomery dataset:
.. code:: sh
- ptbench train -vv pasa montgomery --batch-size=4 --epochs=150
+ mednet train -vv pasa montgomery --batch-size=4 --epochs=150
To train DensenetRS CNN on the NIH CXR14 dataset:
.. code:: sh
- ptbench train -vv nih_cxr14 densenet_rs --batch-size=8 --epochs=10
+ mednet train -vv nih_cxr14 densenet_rs --batch-size=8 --epochs=10
Logistic regressor or shallow network
-------------------------------------
To train a logistic regressor or a shallow network, use the command-line
-interface (CLI) application ``ptbench train``, available on your prompt. To use
+interface (CLI) application ``mednet train``, available on your prompt. To use
this CLI, you must define the input dataset that will be used to train the
model, as well as the type of model that will be trained.
-You may issue ``ptbench train --help`` for a help message containing more
+You may issue ``mednet train --help`` for a help message containing more
detailed instructions.
Examples
@@ -58,7 +58,7 @@ Montgomery dataset:
.. code:: sh
- ptbench train -vv logistic_regression montgomery_rs --batch-size=4 --epochs=20
+ mednet train -vv logistic_regression montgomery_rs --batch-size=4 --epochs=20
To train an multi-layer perceptron (MLP) using predictions from a densenet
@@ -67,7 +67,7 @@ dataset:
.. code:: sh
- ptbench train -vv mlp shenzhen_rs --batch-size=4 --epochs=20
+ mednet train -vv mlp shenzhen_rs --batch-size=4 --epochs=20
.. include:: ../links.rst
diff --git a/pyproject.toml b/pyproject.toml
index 16082e2d..0bf3ed8f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
-name = "ptbench"
+name = "mednet"
version = "1.0.0b0"
requires-python = ">=3.10"
description = "Benchmarks for Computer-Aided Disease Detection from Medical Data."
@@ -45,10 +45,10 @@ dependencies = [
]
[project.urls]
-documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/ptbench/main/sphinx/"
-homepage = "https://pypi.org/project/ptbench"
-repository = "https://gitlab.idiap.ch/biosignal/software/ptbench"
-changelog = "https://gitlab.idiap.ch/biosignal/software/ptbench/-/releases"
+documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/mednet/main/sphinx/"
+homepage = "https://pypi.org/project/mednet"
+repository = "https://gitlab.idiap.ch/biosignal/software/mednet"
+changelog = "https://gitlab.idiap.ch/biosignal/software/mednet/-/releases"
[project.optional-dependencies]
qa = ["pre-commit"]
@@ -64,173 +64,173 @@ doc = [
test = ["pytest", "pytest-cov", "coverage"]
[project.scripts]
-ptbench = "ptbench.scripts.cli:cli"
+mednet = "mednet.scripts.cli:cli"
-[project.entry-points."ptbench.config"]
+[project.entry-points."mednet.config"]
# models
-pasa = "ptbench.config.models.pasa"
-mlp = "ptbench.config.models.mlp"
-logistic-regression = "ptbench.config.models.logistic_regression"
-alexnet = "ptbench.config.models.alexnet"
-alexnet-pretrained = "ptbench.config.models.alexnet_pretrained"
-densenet = "ptbench.config.models.densenet"
-densenet-pretrained = "ptbench.config.models.densenet_pretrained"
+pasa = "mednet.config.models.pasa"
+mlp = "mednet.config.models.mlp"
+logistic-regression = "mednet.config.models.logistic_regression"
+alexnet = "mednet.config.models.alexnet"
+alexnet-pretrained = "mednet.config.models.alexnet_pretrained"
+densenet = "mednet.config.models.densenet"
+densenet-pretrained = "mednet.config.models.densenet_pretrained"
# montgomery dataset (and cross-validation folds)
-montgomery = "ptbench.config.data.montgomery.default"
-montgomery-f0 = "ptbench.config.data.montgomery.fold_0"
-montgomery-f1 = "ptbench.config.data.montgomery.fold_1"
-montgomery-f2 = "ptbench.config.data.montgomery.fold_2"
-montgomery-f3 = "ptbench.config.data.montgomery.fold_3"
-montgomery-f4 = "ptbench.config.data.montgomery.fold_4"
-montgomery-f5 = "ptbench.config.data.montgomery.fold_5"
-montgomery-f6 = "ptbench.config.data.montgomery.fold_6"
-montgomery-f7 = "ptbench.config.data.montgomery.fold_7"
-montgomery-f8 = "ptbench.config.data.montgomery.fold_8"
-montgomery-f9 = "ptbench.config.data.montgomery.fold_9"
+montgomery = "mednet.config.data.montgomery.default"
+montgomery-f0 = "mednet.config.data.montgomery.fold_0"
+montgomery-f1 = "mednet.config.data.montgomery.fold_1"
+montgomery-f2 = "mednet.config.data.montgomery.fold_2"
+montgomery-f3 = "mednet.config.data.montgomery.fold_3"
+montgomery-f4 = "mednet.config.data.montgomery.fold_4"
+montgomery-f5 = "mednet.config.data.montgomery.fold_5"
+montgomery-f6 = "mednet.config.data.montgomery.fold_6"
+montgomery-f7 = "mednet.config.data.montgomery.fold_7"
+montgomery-f8 = "mednet.config.data.montgomery.fold_8"
+montgomery-f9 = "mednet.config.data.montgomery.fold_9"
# shenzhen dataset (and cross-validation folds)
-shenzhen = "ptbench.config.data.shenzhen.default"
-shenzhen-f0 = "ptbench.config.data.shenzhen.fold_0"
-shenzhen-f1 = "ptbench.config.data.shenzhen.fold_1"
-shenzhen-f2 = "ptbench.config.data.shenzhen.fold_2"
-shenzhen-f3 = "ptbench.config.data.shenzhen.fold_3"
-shenzhen-f4 = "ptbench.config.data.shenzhen.fold_4"
-shenzhen-f5 = "ptbench.config.data.shenzhen.fold_5"
-shenzhen-f6 = "ptbench.config.data.shenzhen.fold_6"
-shenzhen-f7 = "ptbench.config.data.shenzhen.fold_7"
-shenzhen-f8 = "ptbench.config.data.shenzhen.fold_8"
-shenzhen-f9 = "ptbench.config.data.shenzhen.fold_9"
+shenzhen = "mednet.config.data.shenzhen.default"
+shenzhen-f0 = "mednet.config.data.shenzhen.fold_0"
+shenzhen-f1 = "mednet.config.data.shenzhen.fold_1"
+shenzhen-f2 = "mednet.config.data.shenzhen.fold_2"
+shenzhen-f3 = "mednet.config.data.shenzhen.fold_3"
+shenzhen-f4 = "mednet.config.data.shenzhen.fold_4"
+shenzhen-f5 = "mednet.config.data.shenzhen.fold_5"
+shenzhen-f6 = "mednet.config.data.shenzhen.fold_6"
+shenzhen-f7 = "mednet.config.data.shenzhen.fold_7"
+shenzhen-f8 = "mednet.config.data.shenzhen.fold_8"
+shenzhen-f9 = "mednet.config.data.shenzhen.fold_9"
# indian dataset (and cross-validation folds)
-indian = "ptbench.config.data.indian.default"
-indian-f0 = "ptbench.config.data.indian.fold_0"
-indian-f1 = "ptbench.config.data.indian.fold_1"
-indian-f2 = "ptbench.config.data.indian.fold_2"
-indian-f3 = "ptbench.config.data.indian.fold_3"
-indian-f4 = "ptbench.config.data.indian.fold_4"
-indian-f5 = "ptbench.config.data.indian.fold_5"
-indian-f6 = "ptbench.config.data.indian.fold_6"
-indian-f7 = "ptbench.config.data.indian.fold_7"
-indian-f8 = "ptbench.config.data.indian.fold_8"
-indian-f9 = "ptbench.config.data.indian.fold_9"
+indian = "mednet.config.data.indian.default"
+indian-f0 = "mednet.config.data.indian.fold_0"
+indian-f1 = "mednet.config.data.indian.fold_1"
+indian-f2 = "mednet.config.data.indian.fold_2"
+indian-f3 = "mednet.config.data.indian.fold_3"
+indian-f4 = "mednet.config.data.indian.fold_4"
+indian-f5 = "mednet.config.data.indian.fold_5"
+indian-f6 = "mednet.config.data.indian.fold_6"
+indian-f7 = "mednet.config.data.indian.fold_7"
+indian-f8 = "mednet.config.data.indian.fold_8"
+indian-f9 = "mednet.config.data.indian.fold_9"
# TBX11K dataset split 1: healthy vs active tb, and cross-validation folds
-tbx11k-v1-healthy-vs-atb = "ptbench.config.data.tbx11k.v1_healthy_vs_atb"
-tbx11k-v1-f0 = "ptbench.config.data.tbx11k.v1_fold_0"
-tbx11k-v1-f1 = "ptbench.config.data.tbx11k.v1_fold_1"
-tbx11k-v1-f2 = "ptbench.config.data.tbx11k.v1_fold_2"
-tbx11k-v1-f3 = "ptbench.config.data.tbx11k.v1_fold_3"
-tbx11k-v1-f4 = "ptbench.config.data.tbx11k.v1_fold_4"
-tbx11k-v1-f5 = "ptbench.config.data.tbx11k.v1_fold_5"
-tbx11k-v1-f6 = "ptbench.config.data.tbx11k.v1_fold_6"
-tbx11k-v1-f7 = "ptbench.config.data.tbx11k.v1_fold_7"
-tbx11k-v1-f8 = "ptbench.config.data.tbx11k.v1_fold_8"
-tbx11k-v1-f9 = "ptbench.config.data.tbx11k.v1_fold_9"
+tbx11k-v1-healthy-vs-atb = "mednet.config.data.tbx11k.v1_healthy_vs_atb"
+tbx11k-v1-f0 = "mednet.config.data.tbx11k.v1_fold_0"
+tbx11k-v1-f1 = "mednet.config.data.tbx11k.v1_fold_1"
+tbx11k-v1-f2 = "mednet.config.data.tbx11k.v1_fold_2"
+tbx11k-v1-f3 = "mednet.config.data.tbx11k.v1_fold_3"
+tbx11k-v1-f4 = "mednet.config.data.tbx11k.v1_fold_4"
+tbx11k-v1-f5 = "mednet.config.data.tbx11k.v1_fold_5"
+tbx11k-v1-f6 = "mednet.config.data.tbx11k.v1_fold_6"
+tbx11k-v1-f7 = "mednet.config.data.tbx11k.v1_fold_7"
+tbx11k-v1-f8 = "mednet.config.data.tbx11k.v1_fold_8"
+tbx11k-v1-f9 = "mednet.config.data.tbx11k.v1_fold_9"
# TBX11K dataset split 2: others vs active tb, and cross-validation folds
-tbx11k-v2-others-vs-atb = "ptbench.config.data.tbx11k.v2_others_vs_atb"
-tbx11k-v2-f0 = "ptbench.config.data.tbx11k.v2_fold_0"
-tbx11k-v2-f1 = "ptbench.config.data.tbx11k.v2_fold_1"
-tbx11k-v2-f2 = "ptbench.config.data.tbx11k.v2_fold_2"
-tbx11k-v2-f3 = "ptbench.config.data.tbx11k.v2_fold_3"
-tbx11k-v2-f4 = "ptbench.config.data.tbx11k.v2_fold_4"
-tbx11k-v2-f5 = "ptbench.config.data.tbx11k.v2_fold_5"
-tbx11k-v2-f6 = "ptbench.config.data.tbx11k.v2_fold_6"
-tbx11k-v2-f7 = "ptbench.config.data.tbx11k.v2_fold_7"
-tbx11k-v2-f8 = "ptbench.config.data.tbx11k.v2_fold_8"
-tbx11k-v2-f9 = "ptbench.config.data.tbx11k.v2_fold_9"
+tbx11k-v2-others-vs-atb = "mednet.config.data.tbx11k.v2_others_vs_atb"
+tbx11k-v2-f0 = "mednet.config.data.tbx11k.v2_fold_0"
+tbx11k-v2-f1 = "mednet.config.data.tbx11k.v2_fold_1"
+tbx11k-v2-f2 = "mednet.config.data.tbx11k.v2_fold_2"
+tbx11k-v2-f3 = "mednet.config.data.tbx11k.v2_fold_3"
+tbx11k-v2-f4 = "mednet.config.data.tbx11k.v2_fold_4"
+tbx11k-v2-f5 = "mednet.config.data.tbx11k.v2_fold_5"
+tbx11k-v2-f6 = "mednet.config.data.tbx11k.v2_fold_6"
+tbx11k-v2-f7 = "mednet.config.data.tbx11k.v2_fold_7"
+tbx11k-v2-f8 = "mednet.config.data.tbx11k.v2_fold_8"
+tbx11k-v2-f9 = "mednet.config.data.tbx11k.v2_fold_9"
# montgomery-shenzhen aggregated dataset
-montgomery-shenzhen = "ptbench.config.data.montgomery_shenzhen.default"
-montgomery-shenzhen-f0 = "ptbench.config.data.montgomery_shenzhen.fold_0"
-montgomery-shenzhen-f1 = "ptbench.config.data.montgomery_shenzhen.fold_1"
-montgomery-shenzhen-f2 = "ptbench.config.data.montgomery_shenzhen.fold_2"
-montgomery-shenzhen-f3 = "ptbench.config.data.montgomery_shenzhen.fold_3"
-montgomery-shenzhen-f4 = "ptbench.config.data.montgomery_shenzhen.fold_4"
-montgomery-shenzhen-f5 = "ptbench.config.data.montgomery_shenzhen.fold_5"
-montgomery-shenzhen-f6 = "ptbench.config.data.montgomery_shenzhen.fold_6"
-montgomery-shenzhen-f7 = "ptbench.config.data.montgomery_shenzhen.fold_7"
-montgomery-shenzhen-f8 = "ptbench.config.data.montgomery_shenzhen.fold_8"
-montgomery-shenzhen-f9 = "ptbench.config.data.montgomery_shenzhen.fold_9"
+montgomery-shenzhen = "mednet.config.data.montgomery_shenzhen.default"
+montgomery-shenzhen-f0 = "mednet.config.data.montgomery_shenzhen.fold_0"
+montgomery-shenzhen-f1 = "mednet.config.data.montgomery_shenzhen.fold_1"
+montgomery-shenzhen-f2 = "mednet.config.data.montgomery_shenzhen.fold_2"
+montgomery-shenzhen-f3 = "mednet.config.data.montgomery_shenzhen.fold_3"
+montgomery-shenzhen-f4 = "mednet.config.data.montgomery_shenzhen.fold_4"
+montgomery-shenzhen-f5 = "mednet.config.data.montgomery_shenzhen.fold_5"
+montgomery-shenzhen-f6 = "mednet.config.data.montgomery_shenzhen.fold_6"
+montgomery-shenzhen-f7 = "mednet.config.data.montgomery_shenzhen.fold_7"
+montgomery-shenzhen-f8 = "mednet.config.data.montgomery_shenzhen.fold_8"
+montgomery-shenzhen-f9 = "mednet.config.data.montgomery_shenzhen.fold_9"
# montgomery-shenzhen-indian aggregated dataset
-montgomery-shenzhen-indian = "ptbench.config.data.montgomery_shenzhen_indian.default"
-montgomery-shenzhen-indian-f0 = "ptbench.config.data.montgomery_shenzhen_indian.fold_0"
-montgomery-shenzhen-indian-f1 = "ptbench.config.data.montgomery_shenzhen_indian.fold_1"
-montgomery-shenzhen-indian-f2 = "ptbench.config.data.montgomery_shenzhen_indian.fold_2"
-montgomery-shenzhen-indian-f3 = "ptbench.config.data.montgomery_shenzhen_indian.fold_3"
-montgomery-shenzhen-indian-f4 = "ptbench.config.data.montgomery_shenzhen_indian.fold_4"
-montgomery-shenzhen-indian-f5 = "ptbench.config.data.montgomery_shenzhen_indian.fold_5"
-montgomery-shenzhen-indian-f6 = "ptbench.config.data.montgomery_shenzhen_indian.fold_6"
-montgomery-shenzhen-indian-f7 = "ptbench.config.data.montgomery_shenzhen_indian.fold_7"
-montgomery-shenzhen-indian-f8 = "ptbench.config.data.montgomery_shenzhen_indian.fold_8"
-montgomery-shenzhen-indian-f9 = "ptbench.config.data.montgomery_shenzhen_indian.fold_9"
+montgomery-shenzhen-indian = "mednet.config.data.montgomery_shenzhen_indian.default"
+montgomery-shenzhen-indian-f0 = "mednet.config.data.montgomery_shenzhen_indian.fold_0"
+montgomery-shenzhen-indian-f1 = "mednet.config.data.montgomery_shenzhen_indian.fold_1"
+montgomery-shenzhen-indian-f2 = "mednet.config.data.montgomery_shenzhen_indian.fold_2"
+montgomery-shenzhen-indian-f3 = "mednet.config.data.montgomery_shenzhen_indian.fold_3"
+montgomery-shenzhen-indian-f4 = "mednet.config.data.montgomery_shenzhen_indian.fold_4"
+montgomery-shenzhen-indian-f5 = "mednet.config.data.montgomery_shenzhen_indian.fold_5"
+montgomery-shenzhen-indian-f6 = "mednet.config.data.montgomery_shenzhen_indian.fold_6"
+montgomery-shenzhen-indian-f7 = "mednet.config.data.montgomery_shenzhen_indian.fold_7"
+montgomery-shenzhen-indian-f8 = "mednet.config.data.montgomery_shenzhen_indian.fold_8"
+montgomery-shenzhen-indian-f9 = "mednet.config.data.montgomery_shenzhen_indian.fold_9"
# montgomery-shenzhen-indian-tbx11k aggregated dataset
-montgomery-shenzhen-indian-tbx11k-v1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v1-f0 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0"
-montgomery-shenzhen-indian-tbx11k-v1-f1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1"
-montgomery-shenzhen-indian-tbx11k-v1-f2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2"
-montgomery-shenzhen-indian-tbx11k-v1-f3 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3"
-montgomery-shenzhen-indian-tbx11k-v1-f4 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4"
-montgomery-shenzhen-indian-tbx11k-v1-f5 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5"
-montgomery-shenzhen-indian-tbx11k-v1-f6 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6"
-montgomery-shenzhen-indian-tbx11k-v1-f7 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7"
-montgomery-shenzhen-indian-tbx11k-v1-f8 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8"
-montgomery-shenzhen-indian-tbx11k-v1-f9 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9"
-montgomery-shenzhen-indian-tbx11k-v2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v2-f0 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0"
-montgomery-shenzhen-indian-tbx11k-v2-f1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1"
-montgomery-shenzhen-indian-tbx11k-v2-f2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2"
-montgomery-shenzhen-indian-tbx11k-v2-f3 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3"
-montgomery-shenzhen-indian-tbx11k-v2-f4 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4"
-montgomery-shenzhen-indian-tbx11k-v2-f5 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5"
-montgomery-shenzhen-indian-tbx11k-v2-f6 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6"
-montgomery-shenzhen-indian-tbx11k-v2-f7 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7"
-montgomery-shenzhen-indian-tbx11k-v2-f8 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8"
-montgomery-shenzhen-indian-tbx11k-v2-f9 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9"
+montgomery-shenzhen-indian-tbx11k-v1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb"
+montgomery-shenzhen-indian-tbx11k-v1-f0 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0"
+montgomery-shenzhen-indian-tbx11k-v1-f1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1"
+montgomery-shenzhen-indian-tbx11k-v1-f2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2"
+montgomery-shenzhen-indian-tbx11k-v1-f3 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3"
+montgomery-shenzhen-indian-tbx11k-v1-f4 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4"
+montgomery-shenzhen-indian-tbx11k-v1-f5 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5"
+montgomery-shenzhen-indian-tbx11k-v1-f6 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6"
+montgomery-shenzhen-indian-tbx11k-v1-f7 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7"
+montgomery-shenzhen-indian-tbx11k-v1-f8 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8"
+montgomery-shenzhen-indian-tbx11k-v1-f9 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9"
+montgomery-shenzhen-indian-tbx11k-v2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb"
+montgomery-shenzhen-indian-tbx11k-v2-f0 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0"
+montgomery-shenzhen-indian-tbx11k-v2-f1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1"
+montgomery-shenzhen-indian-tbx11k-v2-f2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2"
+montgomery-shenzhen-indian-tbx11k-v2-f3 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3"
+montgomery-shenzhen-indian-tbx11k-v2-f4 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4"
+montgomery-shenzhen-indian-tbx11k-v2-f5 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5"
+montgomery-shenzhen-indian-tbx11k-v2-f6 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6"
+montgomery-shenzhen-indian-tbx11k-v2-f7 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7"
+montgomery-shenzhen-indian-tbx11k-v2-f8 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8"
+montgomery-shenzhen-indian-tbx11k-v2-f9 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9"
# tbpoc dataset (only cross-validation folds)
-tbpoc-f0 = "ptbench.config.data.tbpoc.fold_0"
-tbpoc-f1 = "ptbench.config.data.tbpoc.fold_1"
-tbpoc-f2 = "ptbench.config.data.tbpoc.fold_2"
-tbpoc-f3 = "ptbench.config.data.tbpoc.fold_3"
-tbpoc-f4 = "ptbench.config.data.tbpoc.fold_4"
-tbpoc-f5 = "ptbench.config.data.tbpoc.fold_5"
-tbpoc-f6 = "ptbench.config.data.tbpoc.fold_6"
-tbpoc-f7 = "ptbench.config.data.tbpoc.fold_7"
-tbpoc-f8 = "ptbench.config.data.tbpoc.fold_8"
-tbpoc-f9 = "ptbench.config.data.tbpoc.fold_9"
+tbpoc-f0 = "mednet.config.data.tbpoc.fold_0"
+tbpoc-f1 = "mednet.config.data.tbpoc.fold_1"
+tbpoc-f2 = "mednet.config.data.tbpoc.fold_2"
+tbpoc-f3 = "mednet.config.data.tbpoc.fold_3"
+tbpoc-f4 = "mednet.config.data.tbpoc.fold_4"
+tbpoc-f5 = "mednet.config.data.tbpoc.fold_5"
+tbpoc-f6 = "mednet.config.data.tbpoc.fold_6"
+tbpoc-f7 = "mednet.config.data.tbpoc.fold_7"
+tbpoc-f8 = "mednet.config.data.tbpoc.fold_8"
+tbpoc-f9 = "mednet.config.data.tbpoc.fold_9"
# hivtb dataset (only cross-validation folds)
-hivtb-f0 = "ptbench.config.data.hivtb.fold_0"
-hivtb-f1 = "ptbench.config.data.hivtb.fold_1"
-hivtb-f2 = "ptbench.config.data.hivtb.fold_2"
-hivtb-f3 = "ptbench.config.data.hivtb.fold_3"
-hivtb-f4 = "ptbench.config.data.hivtb.fold_4"
-hivtb-f5 = "ptbench.config.data.hivtb.fold_5"
-hivtb-f6 = "ptbench.config.data.hivtb.fold_6"
-hivtb-f7 = "ptbench.config.data.hivtb.fold_7"
-hivtb-f8 = "ptbench.config.data.hivtb.fold_8"
-hivtb-f9 = "ptbench.config.data.hivtb.fold_9"
+hivtb-f0 = "mednet.config.data.hivtb.fold_0"
+hivtb-f1 = "mednet.config.data.hivtb.fold_1"
+hivtb-f2 = "mednet.config.data.hivtb.fold_2"
+hivtb-f3 = "mednet.config.data.hivtb.fold_3"
+hivtb-f4 = "mednet.config.data.hivtb.fold_4"
+hivtb-f5 = "mednet.config.data.hivtb.fold_5"
+hivtb-f6 = "mednet.config.data.hivtb.fold_6"
+hivtb-f7 = "mednet.config.data.hivtb.fold_7"
+hivtb-f8 = "mednet.config.data.hivtb.fold_8"
+hivtb-f9 = "mednet.config.data.hivtb.fold_9"
# NIH CXR14 (relabeled), multi-class (14 labels)
-nih-cxr14 = "ptbench.config.data.nih_cxr14.default"
-nih-cxr14-cardiomegaly = "ptbench.config.data.nih_cxr14.cardiomegaly"
+nih-cxr14 = "mednet.config.data.nih_cxr14.default"
+nih-cxr14-cardiomegaly = "mednet.config.data.nih_cxr14.cardiomegaly"
# PadChest, multi-class (varied number of labels)
-padchest-idiap = "ptbench.config.data.padchest.idiap"
-padchest-tb-idiap = "ptbench.config.data.padchest.tb_idiap"
-padchest-no-tb-idiap = "ptbench.config.data.padchest.no_tb_idiap"
-padchest-cardiomegaly-idiap = "ptbench.config.data.padchest.cardiomegaly_idiap"
+padchest-idiap = "mednet.config.data.padchest.idiap"
+padchest-tb-idiap = "mednet.config.data.padchest.tb_idiap"
+padchest-no-tb-idiap = "mednet.config.data.padchest.no_tb_idiap"
+padchest-cardiomegaly-idiap = "mednet.config.data.padchest.cardiomegaly_idiap"
# NIH CXR14 / PadChest aggregated dataset
-nih-cxr14-padchest = "ptbench.config.data.nih_cxr14_padchest.idiap"
+nih-cxr14-padchest = "mednet.config.data.nih_cxr14_padchest.idiap"
# montgomery-shenzhen-indian-padchest aggregated dataset
-montgomery-shenzhen-indian-padchest = "ptbench.config.data.montgomery_shenzhen_indian_padchest.default"
+montgomery-shenzhen-indian-padchest = "mednet.config.data.montgomery_shenzhen_indian_padchest.default"
[tool.setuptools]
zip-safe = true
@@ -252,6 +252,6 @@ lines_between_types = 1
line-length = 80
[tool.pytest.ini_options]
-addopts = ["--cov=ptbench", "--cov-report=term-missing", "--import-mode=append"]
+addopts = ["--cov=mednet", "--cov-report=term-missing", "--import-mode=append"]
junit_logging = "all"
junit_log_passing_tests = false
diff --git a/src/ptbench/__init__.py b/src/mednet/__init__.py
similarity index 100%
rename from src/ptbench/__init__.py
rename to src/mednet/__init__.py
diff --git a/src/ptbench/config/__init__.py b/src/mednet/config/__init__.py
similarity index 100%
rename from src/ptbench/config/__init__.py
rename to src/mednet/config/__init__.py
diff --git a/src/ptbench/config/data/__init__.py b/src/mednet/config/data/__init__.py
similarity index 100%
rename from src/ptbench/config/data/__init__.py
rename to src/mednet/config/data/__init__.py
diff --git a/src/ptbench/config/data/hivtb/__init__.py b/src/mednet/config/data/hivtb/__init__.py
similarity index 100%
rename from src/ptbench/config/data/hivtb/__init__.py
rename to src/mednet/config/data/hivtb/__init__.py
diff --git a/src/ptbench/config/data/hivtb/datamodule.py b/src/mednet/config/data/hivtb/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/hivtb/datamodule.py
rename to src/mednet/config/data/hivtb/datamodule.py
index 653743a5..d5bf8103 100644
--- a/src/ptbench/config/data/hivtb/datamodule.py
+++ b/src/mednet/config/data/hivtb/datamodule.py
@@ -14,13 +14,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/hivtb/fold-0.json b/src/mednet/config/data/hivtb/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-0.json
rename to src/mednet/config/data/hivtb/fold-0.json
diff --git a/src/ptbench/config/data/hivtb/fold-1.json b/src/mednet/config/data/hivtb/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-1.json
rename to src/mednet/config/data/hivtb/fold-1.json
diff --git a/src/ptbench/config/data/hivtb/fold-2.json b/src/mednet/config/data/hivtb/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-2.json
rename to src/mednet/config/data/hivtb/fold-2.json
diff --git a/src/ptbench/config/data/hivtb/fold-3.json b/src/mednet/config/data/hivtb/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-3.json
rename to src/mednet/config/data/hivtb/fold-3.json
diff --git a/src/ptbench/config/data/hivtb/fold-4.json b/src/mednet/config/data/hivtb/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-4.json
rename to src/mednet/config/data/hivtb/fold-4.json
diff --git a/src/ptbench/config/data/hivtb/fold-5.json b/src/mednet/config/data/hivtb/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-5.json
rename to src/mednet/config/data/hivtb/fold-5.json
diff --git a/src/ptbench/config/data/hivtb/fold-6.json b/src/mednet/config/data/hivtb/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-6.json
rename to src/mednet/config/data/hivtb/fold-6.json
diff --git a/src/ptbench/config/data/hivtb/fold-7.json b/src/mednet/config/data/hivtb/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-7.json
rename to src/mednet/config/data/hivtb/fold-7.json
diff --git a/src/ptbench/config/data/hivtb/fold-8.json b/src/mednet/config/data/hivtb/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-8.json
rename to src/mednet/config/data/hivtb/fold-8.json
diff --git a/src/ptbench/config/data/hivtb/fold-9.json b/src/mednet/config/data/hivtb/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-9.json
rename to src/mednet/config/data/hivtb/fold-9.json
diff --git a/src/ptbench/config/data/hivtb/fold_0.py b/src/mednet/config/data/hivtb/fold_0.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_0.py
rename to src/mednet/config/data/hivtb/fold_0.py
index 4e00590f..fb3a4c74 100644
--- a/src/ptbench/config/data/hivtb/fold_0.py
+++ b/src/mednet/config/data/hivtb/fold_0.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/hivtb/fold_1.py b/src/mednet/config/data/hivtb/fold_1.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_1.py
rename to src/mednet/config/data/hivtb/fold_1.py
index 55333dd0..65013671 100644
--- a/src/ptbench/config/data/hivtb/fold_1.py
+++ b/src/mednet/config/data/hivtb/fold_1.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/hivtb/fold_2.py b/src/mednet/config/data/hivtb/fold_2.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_2.py
rename to src/mednet/config/data/hivtb/fold_2.py
index 5c8fd9b7..0436ae41 100644
--- a/src/ptbench/config/data/hivtb/fold_2.py
+++ b/src/mednet/config/data/hivtb/fold_2.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/hivtb/fold_3.py b/src/mednet/config/data/hivtb/fold_3.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_3.py
rename to src/mednet/config/data/hivtb/fold_3.py
index 5d1b308c..b657bb47 100644
--- a/src/ptbench/config/data/hivtb/fold_3.py
+++ b/src/mednet/config/data/hivtb/fold_3.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/hivtb/fold_4.py b/src/mednet/config/data/hivtb/fold_4.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_4.py
rename to src/mednet/config/data/hivtb/fold_4.py
index 77c2073a..92654218 100644
--- a/src/ptbench/config/data/hivtb/fold_4.py
+++ b/src/mednet/config/data/hivtb/fold_4.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/hivtb/fold_5.py b/src/mednet/config/data/hivtb/fold_5.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_5.py
rename to src/mednet/config/data/hivtb/fold_5.py
index e06f9dd1..9cce77de 100644
--- a/src/ptbench/config/data/hivtb/fold_5.py
+++ b/src/mednet/config/data/hivtb/fold_5.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/hivtb/fold_6.py b/src/mednet/config/data/hivtb/fold_6.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_6.py
rename to src/mednet/config/data/hivtb/fold_6.py
index 4b7db6de..b52509a8 100644
--- a/src/ptbench/config/data/hivtb/fold_6.py
+++ b/src/mednet/config/data/hivtb/fold_6.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/hivtb/fold_7.py b/src/mednet/config/data/hivtb/fold_7.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_7.py
rename to src/mednet/config/data/hivtb/fold_7.py
index 3670047c..c2af009c 100644
--- a/src/ptbench/config/data/hivtb/fold_7.py
+++ b/src/mednet/config/data/hivtb/fold_7.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/hivtb/fold_8.py b/src/mednet/config/data/hivtb/fold_8.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_8.py
rename to src/mednet/config/data/hivtb/fold_8.py
index c0900d15..b76fda84 100644
--- a/src/ptbench/config/data/hivtb/fold_8.py
+++ b/src/mednet/config/data/hivtb/fold_8.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/hivtb/fold_9.py b/src/mednet/config/data/hivtb/fold_9.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_9.py
rename to src/mednet/config/data/hivtb/fold_9.py
index 96ceb596..c2c92410 100644
--- a/src/ptbench/config/data/hivtb/fold_9.py
+++ b/src/mednet/config/data/hivtb/fold_9.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/indian/__init__.py b/src/mednet/config/data/indian/__init__.py
similarity index 100%
rename from src/ptbench/config/data/indian/__init__.py
rename to src/mednet/config/data/indian/__init__.py
diff --git a/src/ptbench/config/data/indian/datamodule.py b/src/mednet/config/data/indian/datamodule.py
similarity index 90%
rename from src/ptbench/config/data/indian/datamodule.py
rename to src/mednet/config/data/indian/datamodule.py
index 1c514f47..c8b762fc 100644
--- a/src/ptbench/config/data/indian/datamodule.py
+++ b/src/mednet/config/data/indian/datamodule.py
@@ -8,10 +8,10 @@ Database reference: [INDIAN-2013]_
import importlib.resources
-from ptbench.config.data.shenzhen.datamodule import RawDataLoader
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
+from ....config.data.shenzhen.datamodule import RawDataLoader
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/indian/default.json b/src/mednet/config/data/indian/default.json
similarity index 100%
rename from src/ptbench/config/data/indian/default.json
rename to src/mednet/config/data/indian/default.json
diff --git a/src/ptbench/config/data/indian/default.py b/src/mednet/config/data/indian/default.py
similarity index 65%
rename from src/ptbench/config/data/indian/default.py
rename to src/mednet/config/data/indian/default.py
index 33bcb48d..9c402b8e 100644
--- a/src/ptbench/config/data/indian/default.py
+++ b/src/mednet/config/data/indian/default.py
@@ -5,9 +5,9 @@
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/indian/fold-0.json b/src/mednet/config/data/indian/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-0.json
rename to src/mednet/config/data/indian/fold-0.json
diff --git a/src/ptbench/config/data/indian/fold-1.json b/src/mednet/config/data/indian/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-1.json
rename to src/mednet/config/data/indian/fold-1.json
diff --git a/src/ptbench/config/data/indian/fold-2.json b/src/mednet/config/data/indian/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-2.json
rename to src/mednet/config/data/indian/fold-2.json
diff --git a/src/ptbench/config/data/indian/fold-3.json b/src/mednet/config/data/indian/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-3.json
rename to src/mednet/config/data/indian/fold-3.json
diff --git a/src/ptbench/config/data/indian/fold-4.json b/src/mednet/config/data/indian/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-4.json
rename to src/mednet/config/data/indian/fold-4.json
diff --git a/src/ptbench/config/data/indian/fold-5.json b/src/mednet/config/data/indian/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-5.json
rename to src/mednet/config/data/indian/fold-5.json
diff --git a/src/ptbench/config/data/indian/fold-6.json b/src/mednet/config/data/indian/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-6.json
rename to src/mednet/config/data/indian/fold-6.json
diff --git a/src/ptbench/config/data/indian/fold-7.json b/src/mednet/config/data/indian/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-7.json
rename to src/mednet/config/data/indian/fold-7.json
diff --git a/src/ptbench/config/data/indian/fold-8.json b/src/mednet/config/data/indian/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-8.json
rename to src/mednet/config/data/indian/fold-8.json
diff --git a/src/ptbench/config/data/indian/fold-9.json b/src/mednet/config/data/indian/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-9.json
rename to src/mednet/config/data/indian/fold-9.json
diff --git a/src/ptbench/config/data/indian/fold_0.py b/src/mednet/config/data/indian/fold_0.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_0.py
rename to src/mednet/config/data/indian/fold_0.py
index 6a8e6c5b..2c94e91d 100644
--- a/src/ptbench/config/data/indian/fold_0.py
+++ b/src/mednet/config/data/indian/fold_0.py
@@ -6,9 +6,9 @@ fold 0).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/indian/fold_1.py b/src/mednet/config/data/indian/fold_1.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_1.py
rename to src/mednet/config/data/indian/fold_1.py
index 029b6df6..7c7548e2 100644
--- a/src/ptbench/config/data/indian/fold_1.py
+++ b/src/mednet/config/data/indian/fold_1.py
@@ -6,9 +6,9 @@ fold 1).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/indian/fold_2.py b/src/mednet/config/data/indian/fold_2.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_2.py
rename to src/mednet/config/data/indian/fold_2.py
index f54f35e5..b849a518 100644
--- a/src/ptbench/config/data/indian/fold_2.py
+++ b/src/mednet/config/data/indian/fold_2.py
@@ -6,9 +6,9 @@ fold 2).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/indian/fold_3.py b/src/mednet/config/data/indian/fold_3.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_3.py
rename to src/mednet/config/data/indian/fold_3.py
index 0c493592..c992855d 100644
--- a/src/ptbench/config/data/indian/fold_3.py
+++ b/src/mednet/config/data/indian/fold_3.py
@@ -6,9 +6,9 @@ fold 3).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/indian/fold_4.py b/src/mednet/config/data/indian/fold_4.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_4.py
rename to src/mednet/config/data/indian/fold_4.py
index 52a7b792..8385f0fe 100644
--- a/src/ptbench/config/data/indian/fold_4.py
+++ b/src/mednet/config/data/indian/fold_4.py
@@ -6,9 +6,9 @@ fold 4).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/indian/fold_5.py b/src/mednet/config/data/indian/fold_5.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_5.py
rename to src/mednet/config/data/indian/fold_5.py
index 843a1e8c..7ee271dc 100644
--- a/src/ptbench/config/data/indian/fold_5.py
+++ b/src/mednet/config/data/indian/fold_5.py
@@ -6,9 +6,9 @@ fold 5).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/indian/fold_6.py b/src/mednet/config/data/indian/fold_6.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_6.py
rename to src/mednet/config/data/indian/fold_6.py
index 9970d6f6..9d5c0b94 100644
--- a/src/ptbench/config/data/indian/fold_6.py
+++ b/src/mednet/config/data/indian/fold_6.py
@@ -6,9 +6,9 @@ fold 6).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/indian/fold_7.py b/src/mednet/config/data/indian/fold_7.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_7.py
rename to src/mednet/config/data/indian/fold_7.py
index 5bbef8db..912fd422 100644
--- a/src/ptbench/config/data/indian/fold_7.py
+++ b/src/mednet/config/data/indian/fold_7.py
@@ -6,9 +6,9 @@ fold 7).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/indian/fold_8.py b/src/mednet/config/data/indian/fold_8.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_8.py
rename to src/mednet/config/data/indian/fold_8.py
index 0416153f..b01e5426 100644
--- a/src/ptbench/config/data/indian/fold_8.py
+++ b/src/mednet/config/data/indian/fold_8.py
@@ -6,9 +6,9 @@ fold 8).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/indian/fold_9.py b/src/mednet/config/data/indian/fold_9.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_9.py
rename to src/mednet/config/data/indian/fold_9.py
index 3d4df2a5..31510e32 100644
--- a/src/ptbench/config/data/indian/fold_9.py
+++ b/src/mednet/config/data/indian/fold_9.py
@@ -6,9 +6,9 @@ fold 9).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery/__init__.py b/src/mednet/config/data/montgomery/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery/__init__.py
rename to src/mednet/config/data/montgomery/__init__.py
diff --git a/src/ptbench/config/data/montgomery/datamodule.py b/src/mednet/config/data/montgomery/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/montgomery/datamodule.py
rename to src/mednet/config/data/montgomery/datamodule.py
index 84cdbc77..ec1b7c14 100644
--- a/src/ptbench/config/data/montgomery/datamodule.py
+++ b/src/mednet/config/data/montgomery/datamodule.py
@@ -13,13 +13,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/montgomery/default.json b/src/mednet/config/data/montgomery/default.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/default.json
rename to src/mednet/config/data/montgomery/default.json
diff --git a/src/ptbench/config/data/montgomery/default.py b/src/mednet/config/data/montgomery/default.py
similarity index 67%
rename from src/ptbench/config/data/montgomery/default.py
rename to src/mednet/config/data/montgomery/default.py
index fa890210..edd014e8 100644
--- a/src/ptbench/config/data/montgomery/default.py
+++ b/src/mednet/config/data/montgomery/default.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery/fold-0.json b/src/mednet/config/data/montgomery/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-0.json
rename to src/mednet/config/data/montgomery/fold-0.json
diff --git a/src/ptbench/config/data/montgomery/fold-1.json b/src/mednet/config/data/montgomery/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-1.json
rename to src/mednet/config/data/montgomery/fold-1.json
diff --git a/src/ptbench/config/data/montgomery/fold-2.json b/src/mednet/config/data/montgomery/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-2.json
rename to src/mednet/config/data/montgomery/fold-2.json
diff --git a/src/ptbench/config/data/montgomery/fold-3.json b/src/mednet/config/data/montgomery/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-3.json
rename to src/mednet/config/data/montgomery/fold-3.json
diff --git a/src/ptbench/config/data/montgomery/fold-4.json b/src/mednet/config/data/montgomery/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-4.json
rename to src/mednet/config/data/montgomery/fold-4.json
diff --git a/src/ptbench/config/data/montgomery/fold-5.json b/src/mednet/config/data/montgomery/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-5.json
rename to src/mednet/config/data/montgomery/fold-5.json
diff --git a/src/ptbench/config/data/montgomery/fold-6.json b/src/mednet/config/data/montgomery/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-6.json
rename to src/mednet/config/data/montgomery/fold-6.json
diff --git a/src/ptbench/config/data/montgomery/fold-7.json b/src/mednet/config/data/montgomery/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-7.json
rename to src/mednet/config/data/montgomery/fold-7.json
diff --git a/src/ptbench/config/data/montgomery/fold-8.json b/src/mednet/config/data/montgomery/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-8.json
rename to src/mednet/config/data/montgomery/fold-8.json
diff --git a/src/ptbench/config/data/montgomery/fold-9.json b/src/mednet/config/data/montgomery/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-9.json
rename to src/mednet/config/data/montgomery/fold-9.json
diff --git a/src/ptbench/config/data/montgomery/fold_0.py b/src/mednet/config/data/montgomery/fold_0.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_0.py
rename to src/mednet/config/data/montgomery/fold_0.py
index 2f72873e..6d623303 100644
--- a/src/ptbench/config/data/montgomery/fold_0.py
+++ b/src/mednet/config/data/montgomery/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery/fold_1.py b/src/mednet/config/data/montgomery/fold_1.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_1.py
rename to src/mednet/config/data/montgomery/fold_1.py
index e4fd9fe8..649f625f 100644
--- a/src/ptbench/config/data/montgomery/fold_1.py
+++ b/src/mednet/config/data/montgomery/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery/fold_2.py b/src/mednet/config/data/montgomery/fold_2.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_2.py
rename to src/mednet/config/data/montgomery/fold_2.py
index 903154be..28f55b90 100644
--- a/src/ptbench/config/data/montgomery/fold_2.py
+++ b/src/mednet/config/data/montgomery/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery/fold_3.py b/src/mednet/config/data/montgomery/fold_3.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_3.py
rename to src/mednet/config/data/montgomery/fold_3.py
index 27d9ebdd..e357f27e 100644
--- a/src/ptbench/config/data/montgomery/fold_3.py
+++ b/src/mednet/config/data/montgomery/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery/fold_4.py b/src/mednet/config/data/montgomery/fold_4.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_4.py
rename to src/mednet/config/data/montgomery/fold_4.py
index e5379102..57402c01 100644
--- a/src/ptbench/config/data/montgomery/fold_4.py
+++ b/src/mednet/config/data/montgomery/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery/fold_5.py b/src/mednet/config/data/montgomery/fold_5.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_5.py
rename to src/mednet/config/data/montgomery/fold_5.py
index feb8ac45..30b17241 100644
--- a/src/ptbench/config/data/montgomery/fold_5.py
+++ b/src/mednet/config/data/montgomery/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery/fold_6.py b/src/mednet/config/data/montgomery/fold_6.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_6.py
rename to src/mednet/config/data/montgomery/fold_6.py
index e868c726..d8a2a8e2 100644
--- a/src/ptbench/config/data/montgomery/fold_6.py
+++ b/src/mednet/config/data/montgomery/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery/fold_7.py b/src/mednet/config/data/montgomery/fold_7.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_7.py
rename to src/mednet/config/data/montgomery/fold_7.py
index 0415dfba..86d16e0c 100644
--- a/src/ptbench/config/data/montgomery/fold_7.py
+++ b/src/mednet/config/data/montgomery/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery/fold_8.py b/src/mednet/config/data/montgomery/fold_8.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_8.py
rename to src/mednet/config/data/montgomery/fold_8.py
index d00595b0..67a337d2 100644
--- a/src/ptbench/config/data/montgomery/fold_8.py
+++ b/src/mednet/config/data/montgomery/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery/fold_9.py b/src/mednet/config/data/montgomery/fold_9.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_9.py
rename to src/mednet/config/data/montgomery/fold_9.py
index c9158fd1..032cdbfe 100644
--- a/src/ptbench/config/data/montgomery/fold_9.py
+++ b/src/mednet/config/data/montgomery/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/__init__.py b/src/mednet/config/data/montgomery_shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen/datamodule.py b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
similarity index 96%
rename from src/ptbench/config/data/montgomery_shenzhen/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen/datamodule.py
index 0509dd5f..9699f19d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
@@ -2,8 +2,7 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ptbench.data.datamodule import ConcatDataModule
-
+from ....data.datamodule import ConcatDataModule
from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
from ..montgomery.datamodule import make_split as make_montgomery_split
from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
diff --git a/src/ptbench/config/data/montgomery_shenzhen/default.py b/src/mednet/config/data/montgomery_shenzhen/default.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen/default.py
rename to src/mednet/config/data/montgomery_shenzhen/default.py
index 5a9208f4..bc6a1f94 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen/default.py
@@ -7,6 +7,6 @@ split).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_0.py b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_0.py
index 722876a6..31933cf4 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
@@ -7,6 +7,6 @@ validation fold 0).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_1.py b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_1.py
index 81ee4224..8f4b3705 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
@@ -7,6 +7,6 @@ validation fold 1).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_2.py b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_2.py
index afd77ed3..5be0fa63 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
@@ -7,6 +7,6 @@ validation fold 2).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_3.py b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_3.py
index cc1e48a5..4c82b55d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
@@ -7,6 +7,6 @@ validation fold 3).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_4.py b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_4.py
index b20ba0e3..a3514eb4 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
@@ -7,6 +7,6 @@ validation fold 4).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_5.py b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_5.py
index a521e26f..c81d7788 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
@@ -7,6 +7,6 @@ validation fold 5).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_6.py b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_6.py
index 44454a52..69e826a5 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
@@ -7,6 +7,6 @@ validation fold 6).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_7.py b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_7.py
index 95128328..62127246 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
@@ -7,6 +7,6 @@ validation fold 7).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_8.py b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_8.py
index 220ce854..e6d61098 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
@@ -7,6 +7,6 @@ validation fold 8).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_9.py b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_9.py
index 01fc7503..c59826b3 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
@@ -7,6 +7,6 @@ validation fold 9).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
similarity index 70%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
index 0bbb2c3d..20018573 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -4,23 +4,13 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/default.py b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
similarity index 81%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/default.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/default.py
index 691885b1..d4004d4f 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
@@ -7,6 +7,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
index d9df2f75..43991966 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
index e95a72bd..a400b2c5 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
index 1532a9fb..a3fd8dd0 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
index 21605168..671e10fb 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
index 287afbdd..df22c4aa 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
index 52fd19d2..e8504438 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
index 7232f1c3..962d4443 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
index 16ba67fe..bf08e64f 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
index f6d0788e..dbc23e04 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
index b4d9073c..885ffc9b 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
similarity index 70%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index 93d0193f..8414ad94 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -4,29 +4,15 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and PadChest
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.padchest.datamodule import (
- RawDataLoader as PadchestLoader,
-)
-from ptbench.config.data.padchest.datamodule import (
- make_split as make_padchest_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..padchest.datamodule import RawDataLoader as PadchestLoader
+from ..padchest.datamodule import make_split as make_padchest_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
similarity index 73%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
index bc5ca3d8..3922eac6 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
@@ -4,6 +4,8 @@
"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and Padchest
datasets."""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_padchest.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "tb-idiap.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
similarity index 69%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index 97615574..783f7251 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -4,27 +4,15 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.config.data.tbx11k.datamodule import RawDataLoader as TBX11kLoader
-from ptbench.config.data.tbx11k.datamodule import (
- make_split as make_tbx11k_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
+from ..tbx11k.datamodule import RawDataLoader as TBX11kLoader
+from ..tbx11k.datamodule import make_split as make_tbx11k_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
similarity index 85%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
index 47e8c4ba..6d301af0 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
@@ -8,6 +8,6 @@ This remix dataset combines ``fold-0`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-0`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_tbx11k.datamodule import DataModule
datamodule = DataModule("fold-0.json", "v1-fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
index 4bfa7652..f3476877 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-1`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-1`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-1.json", "v1-fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
index 2dbbb18e..ba5e0e29 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-2`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-2`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-2.json", "v1-fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
index 5f808c6a..1af83edf 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-3`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-3`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-3.json", "v1-fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
index dc9ff8d6..0b5aa4c0 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-4`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-4`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-4.json", "v1-fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
index 137b3c82..946554e3 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-5`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-5`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-5.json", "v1-fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
index 50641ffa..29ba981d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-6`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-6`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-6.json", "v1-fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
index 54f9eaa2..a2cf1159 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-7`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-7`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-7.json", "v1-fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
index dbccf38c..bd023982 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-8`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-8`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-8.json", "v1-fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
index cd1b5a71..4c64d089 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-9`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-9`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-9.json", "v1-fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
index 4c75b15e..0ff7a0b4 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
@@ -9,6 +9,8 @@ and Indian datasets with ``v1-healthy-vs-atb`` split of TBX11k (healthy vs.
active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "v1-healthy-vs-atb.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
index 6add82d0..e71fb091 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-0`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-0.json", "v2-fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
index 09ada33a..0e79b6ea 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-1`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-1.json", "v2-fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
index 756fd9a3..02054b28 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-2`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-2.json", "v2-fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
index 8b72d4f3..89ff7a55 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-3`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-3.json", "v2-fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
index 4cb6ece8..0b2fd6d1 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-4`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-4.json", "v2-fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
index c6b8f89e..dc0d7702 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-5`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-5.json", "v2-fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
index 2c093671..dc2b3792 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-6`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-6.json", "v2-fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
index 0a7c37bc..eceb342b 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-7`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-7.json", "v2-fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
index 5cc64e15..e4ff8059 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-8`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-8.json", "v2-fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
index b8998a23..1aeee35e 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-9`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-9.json", "v2-fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
index ccbac352..82a53cbb 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
@@ -9,6 +9,8 @@ and Indian datasets with ``v2-others-vs-atb`` of TBX11k (healthy, sick and
latent TB vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "v2-others-vs-atb.json")
diff --git a/src/ptbench/config/data/nih_cxr14/__init__.py b/src/mednet/config/data/nih_cxr14/__init__.py
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/__init__.py
rename to src/mednet/config/data/nih_cxr14/__init__.py
diff --git a/src/ptbench/config/data/nih_cxr14/cardiomegaly.json b/src/mednet/config/data/nih_cxr14/cardiomegaly.json
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/cardiomegaly.json
rename to src/mednet/config/data/nih_cxr14/cardiomegaly.json
diff --git a/src/ptbench/config/data/nih_cxr14/cardiomegaly.py b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
similarity index 74%
rename from src/ptbench/config/data/nih_cxr14/cardiomegaly.py
rename to src/mednet/config/data/nih_cxr14/cardiomegaly.py
index 77248a47..8be9fde0 100644
--- a/src/ptbench/config/data/nih_cxr14/cardiomegaly.py
+++ b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
@@ -8,10 +8,10 @@ Database reference: [NIH-CXR14-2017]_
This split contains cardiomegaly cases from the NIH CXR14 database.
-See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+See :py:class:`mednet.config.data.nih_cxr14.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.nih_cxr14.datamodule import DataModule
+from mednet.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("cardiomegaly.json")
diff --git a/src/ptbench/config/data/nih_cxr14/datamodule.py b/src/mednet/config/data/nih_cxr14/datamodule.py
similarity index 95%
rename from src/ptbench/config/data/nih_cxr14/datamodule.py
rename to src/mednet/config/data/nih_cxr14/datamodule.py
index 9875985f..9f295626 100644
--- a/src/ptbench/config/data/nih_cxr14/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14/datamodule.py
@@ -13,12 +13,12 @@ import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/nih_cxr14/default.json.bz2 b/src/mednet/config/data/nih_cxr14/default.json.bz2
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/default.json.bz2
rename to src/mednet/config/data/nih_cxr14/default.json.bz2
diff --git a/src/ptbench/config/data/nih_cxr14/default.py b/src/mednet/config/data/nih_cxr14/default.py
similarity index 71%
rename from src/ptbench/config/data/nih_cxr14/default.py
rename to src/mednet/config/data/nih_cxr14/default.py
index 00ac5afd..2fa797be 100644
--- a/src/ptbench/config/data/nih_cxr14/default.py
+++ b/src/mednet/config/data/nih_cxr14/default.py
@@ -7,10 +7,10 @@
* Validation samples: 6350
* Test samples: 4054
-See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+See :py:class:`mednet.config.data.nih_cxr14.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.nih_cxr14.datamodule import DataModule
+from mednet.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("default.json.bz2")
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/__init__.py b/src/mednet/config/data/nih_cxr14_padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14_padchest/__init__.py
rename to src/mednet/config/data/nih_cxr14_padchest/__init__.py
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
similarity index 73%
rename from src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
rename to src/mednet/config/data/nih_cxr14_padchest/datamodule.py
index cd2d8fb2..09fd623f 100644
--- a/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
@@ -2,19 +2,11 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ptbench.config.data.nih_cxr14.datamodule import (
- RawDataLoader as CXR14Loader,
-)
-from ptbench.config.data.nih_cxr14.datamodule import (
- make_split as make_cxr14_split,
-)
-from ptbench.config.data.padchest.datamodule import (
- RawDataLoader as PadchestLoader,
-)
-from ptbench.config.data.padchest.datamodule import (
- make_split as make_padchest_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..nih_cxr14.datamodule import RawDataLoader as CXR14Loader
+from ..nih_cxr14.datamodule import make_split as make_cxr14_split
+from ..padchest.datamodule import RawDataLoader as PadchestLoader
+from ..padchest.datamodule import make_split as make_padchest_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/idiap.py b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
similarity index 81%
rename from src/ptbench/config/data/nih_cxr14_padchest/idiap.py
rename to src/mednet/config/data/nih_cxr14_padchest/idiap.py
index f318b4f7..91d74d9b 100644
--- a/src/ptbench/config/data/nih_cxr14_padchest/idiap.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
@@ -4,6 +4,6 @@
"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized)
datasets (no-tb-idiap split)."""
-from .datamodule import DataModule
+from mednet.data.config.nih_cx14_padchest.datamodule import DataModule
datamodule = DataModule("default.json.bz2", "no-tb-idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/__init__.py b/src/mednet/config/data/padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/padchest/__init__.py
rename to src/mednet/config/data/padchest/__init__.py
diff --git a/src/ptbench/config/data/padchest/cardiomegaly-idiap.json b/src/mednet/config/data/padchest/cardiomegaly-idiap.json
similarity index 100%
rename from src/ptbench/config/data/padchest/cardiomegaly-idiap.json
rename to src/mednet/config/data/padchest/cardiomegaly-idiap.json
diff --git a/src/ptbench/config/data/padchest/cardiomegaly_idiap.py b/src/mednet/config/data/padchest/cardiomegaly_idiap.py
similarity index 77%
rename from src/ptbench/config/data/padchest/cardiomegaly_idiap.py
rename to src/mednet/config/data/padchest/cardiomegaly_idiap.py
index a22cdc08..b8a4c0d0 100644
--- a/src/ptbench/config/data/padchest/cardiomegaly_idiap.py
+++ b/src/mednet/config/data/padchest/cardiomegaly_idiap.py
@@ -9,10 +9,10 @@ This split contains the first 40 images with cardiomegaly, with parameters:
Label = "Normal", MethodLabel = "Physician", Projection = "PA"
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("cardiomegaly-idiap.json")
diff --git a/src/ptbench/config/data/padchest/datamodule.py b/src/mednet/config/data/padchest/datamodule.py
similarity index 96%
rename from src/ptbench/config/data/padchest/datamodule.py
rename to src/mednet/config/data/padchest/datamodule.py
index 0122a429..a065dece 100644
--- a/src/ptbench/config/data/padchest/datamodule.py
+++ b/src/mednet/config/data/padchest/datamodule.py
@@ -14,13 +14,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/padchest/idiap.json.bz2 b/src/mednet/config/data/padchest/idiap.json.bz2
similarity index 100%
rename from src/ptbench/config/data/padchest/idiap.json.bz2
rename to src/mednet/config/data/padchest/idiap.json.bz2
diff --git a/src/ptbench/config/data/padchest/idiap.py b/src/mednet/config/data/padchest/idiap.py
similarity index 77%
rename from src/ptbench/config/data/padchest/idiap.py
rename to src/mednet/config/data/padchest/idiap.py
index be0f9b2f..07afe93e 100644
--- a/src/ptbench/config/data/padchest/idiap.py
+++ b/src/mednet/config/data/padchest/idiap.py
@@ -6,7 +6,7 @@
Database reference: [PADCHEST-2019]_
This split contains all images in the database. Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
* Split reference: ours
@@ -15,6 +15,6 @@ details.
* Test samples: 0
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/no-tb-idiap.json.bz2 b/src/mednet/config/data/padchest/no-tb-idiap.json.bz2
similarity index 100%
rename from src/ptbench/config/data/padchest/no-tb-idiap.json.bz2
rename to src/mednet/config/data/padchest/no-tb-idiap.json.bz2
diff --git a/src/ptbench/config/data/padchest/no_tb_idiap.py b/src/mednet/config/data/padchest/no_tb_idiap.py
similarity index 83%
rename from src/ptbench/config/data/padchest/no_tb_idiap.py
rename to src/mednet/config/data/padchest/no_tb_idiap.py
index 8c2c5fc7..79f05da5 100644
--- a/src/ptbench/config/data/padchest/no_tb_idiap.py
+++ b/src/mednet/config/data/padchest/no_tb_idiap.py
@@ -29,10 +29,10 @@ Database reference: [PADCHEST-2019]_
* edema and consolidation
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("no-tb-idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/tb-idiap.json b/src/mednet/config/data/padchest/tb-idiap.json
similarity index 100%
rename from src/ptbench/config/data/padchest/tb-idiap.json
rename to src/mednet/config/data/padchest/tb-idiap.json
diff --git a/src/ptbench/config/data/padchest/tb_idiap.py b/src/mednet/config/data/padchest/tb_idiap.py
similarity index 80%
rename from src/ptbench/config/data/padchest/tb_idiap.py
rename to src/mednet/config/data/padchest/tb_idiap.py
index c6c4da93..bf625d71 100644
--- a/src/ptbench/config/data/padchest/tb_idiap.py
+++ b/src/mednet/config/data/padchest/tb_idiap.py
@@ -11,10 +11,10 @@ Projection = "PA" and TB cases. Labelling matches those for active TB (binary)
classification datasets.
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("tb-idiap.json")
diff --git a/src/ptbench/config/data/shenzhen/__init__.py b/src/mednet/config/data/shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/config/data/shenzhen/__init__.py
rename to src/mednet/config/data/shenzhen/__init__.py
diff --git a/src/ptbench/config/data/shenzhen/datamodule.py b/src/mednet/config/data/shenzhen/datamodule.py
similarity index 92%
rename from src/ptbench/config/data/shenzhen/datamodule.py
rename to src/mednet/config/data/shenzhen/datamodule.py
index 70c63893..64091794 100644
--- a/src/ptbench/config/data/shenzhen/datamodule.py
+++ b/src/mednet/config/data/shenzhen/datamodule.py
@@ -13,13 +13,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/shenzhen/default.json b/src/mednet/config/data/shenzhen/default.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/default.json
rename to src/mednet/config/data/shenzhen/default.json
diff --git a/src/ptbench/config/data/shenzhen/default.py b/src/mednet/config/data/shenzhen/default.py
similarity index 78%
rename from src/ptbench/config/data/shenzhen/default.py
rename to src/mednet/config/data/shenzhen/default.py
index fd0dbaf1..e2fa24b2 100644
--- a/src/ptbench/config/data/shenzhen/default.py
+++ b/src/mednet/config/data/shenzhen/default.py
@@ -9,10 +9,10 @@ Database reference: [MONTGOMERY-SHENZHEN-2014]_
* Validation samples: 16% of TB and healthy CXR (including labels)
* Test samples: 20% of TB and healthy CXR (including labels)
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/shenzhen/fold-0.json b/src/mednet/config/data/shenzhen/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-0.json
rename to src/mednet/config/data/shenzhen/fold-0.json
diff --git a/src/ptbench/config/data/shenzhen/fold-1.json b/src/mednet/config/data/shenzhen/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-1.json
rename to src/mednet/config/data/shenzhen/fold-1.json
diff --git a/src/ptbench/config/data/shenzhen/fold-2.json b/src/mednet/config/data/shenzhen/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-2.json
rename to src/mednet/config/data/shenzhen/fold-2.json
diff --git a/src/ptbench/config/data/shenzhen/fold-3.json b/src/mednet/config/data/shenzhen/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-3.json
rename to src/mednet/config/data/shenzhen/fold-3.json
diff --git a/src/ptbench/config/data/shenzhen/fold-4.json b/src/mednet/config/data/shenzhen/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-4.json
rename to src/mednet/config/data/shenzhen/fold-4.json
diff --git a/src/ptbench/config/data/shenzhen/fold-5.json b/src/mednet/config/data/shenzhen/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-5.json
rename to src/mednet/config/data/shenzhen/fold-5.json
diff --git a/src/ptbench/config/data/shenzhen/fold-6.json b/src/mednet/config/data/shenzhen/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-6.json
rename to src/mednet/config/data/shenzhen/fold-6.json
diff --git a/src/ptbench/config/data/shenzhen/fold-7.json b/src/mednet/config/data/shenzhen/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-7.json
rename to src/mednet/config/data/shenzhen/fold-7.json
diff --git a/src/ptbench/config/data/shenzhen/fold-8.json b/src/mednet/config/data/shenzhen/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-8.json
rename to src/mednet/config/data/shenzhen/fold-8.json
diff --git a/src/ptbench/config/data/shenzhen/fold-9.json b/src/mednet/config/data/shenzhen/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-9.json
rename to src/mednet/config/data/shenzhen/fold-9.json
diff --git a/src/ptbench/config/data/shenzhen/fold_0.py b/src/mednet/config/data/shenzhen/fold_0.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_0.py
rename to src/mednet/config/data/shenzhen/fold_0.py
index 890250db..17ab27e5 100644
--- a/src/ptbench/config/data/shenzhen/fold_0.py
+++ b/src/mednet/config/data/shenzhen/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_1.py b/src/mednet/config/data/shenzhen/fold_1.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_1.py
rename to src/mednet/config/data/shenzhen/fold_1.py
index ff95e0d0..61ea13aa 100644
--- a/src/ptbench/config/data/shenzhen/fold_1.py
+++ b/src/mednet/config/data/shenzhen/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_2.py b/src/mednet/config/data/shenzhen/fold_2.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_2.py
rename to src/mednet/config/data/shenzhen/fold_2.py
index db16495c..edb92477 100644
--- a/src/ptbench/config/data/shenzhen/fold_2.py
+++ b/src/mednet/config/data/shenzhen/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_3.py b/src/mednet/config/data/shenzhen/fold_3.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_3.py
rename to src/mednet/config/data/shenzhen/fold_3.py
index d0321c86..61800848 100644
--- a/src/ptbench/config/data/shenzhen/fold_3.py
+++ b/src/mednet/config/data/shenzhen/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_4.py b/src/mednet/config/data/shenzhen/fold_4.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_4.py
rename to src/mednet/config/data/shenzhen/fold_4.py
index f6760358..478af2ee 100644
--- a/src/ptbench/config/data/shenzhen/fold_4.py
+++ b/src/mednet/config/data/shenzhen/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_5.py b/src/mednet/config/data/shenzhen/fold_5.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_5.py
rename to src/mednet/config/data/shenzhen/fold_5.py
index 6d77a840..21dcf8ff 100644
--- a/src/ptbench/config/data/shenzhen/fold_5.py
+++ b/src/mednet/config/data/shenzhen/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_6.py b/src/mednet/config/data/shenzhen/fold_6.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_6.py
rename to src/mednet/config/data/shenzhen/fold_6.py
index 3ecd646e..fbc6aac8 100644
--- a/src/ptbench/config/data/shenzhen/fold_6.py
+++ b/src/mednet/config/data/shenzhen/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_7.py b/src/mednet/config/data/shenzhen/fold_7.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_7.py
rename to src/mednet/config/data/shenzhen/fold_7.py
index 61ba5d27..204f7b0b 100644
--- a/src/ptbench/config/data/shenzhen/fold_7.py
+++ b/src/mednet/config/data/shenzhen/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_8.py b/src/mednet/config/data/shenzhen/fold_8.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_8.py
rename to src/mednet/config/data/shenzhen/fold_8.py
index a03121d5..3679fa18 100644
--- a/src/ptbench/config/data/shenzhen/fold_8.py
+++ b/src/mednet/config/data/shenzhen/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_9.py b/src/mednet/config/data/shenzhen/fold_9.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_9.py
rename to src/mednet/config/data/shenzhen/fold_9.py
index 168031c8..32afdbd8 100644
--- a/src/ptbench/config/data/shenzhen/fold_9.py
+++ b/src/mednet/config/data/shenzhen/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/tbpoc/__init__.py b/src/mednet/config/data/tbpoc/__init__.py
similarity index 100%
rename from src/ptbench/config/data/tbpoc/__init__.py
rename to src/mednet/config/data/tbpoc/__init__.py
diff --git a/src/ptbench/config/data/tbpoc/datamodule.py b/src/mednet/config/data/tbpoc/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/tbpoc/datamodule.py
rename to src/mednet/config/data/tbpoc/datamodule.py
index 42a3a10f..ffe59568 100644
--- a/src/ptbench/config/data/tbpoc/datamodule.py
+++ b/src/mednet/config/data/tbpoc/datamodule.py
@@ -9,13 +9,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/tbpoc/fold-0.json b/src/mednet/config/data/tbpoc/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-0.json
rename to src/mednet/config/data/tbpoc/fold-0.json
diff --git a/src/ptbench/config/data/tbpoc/fold-1.json b/src/mednet/config/data/tbpoc/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-1.json
rename to src/mednet/config/data/tbpoc/fold-1.json
diff --git a/src/ptbench/config/data/tbpoc/fold-2.json b/src/mednet/config/data/tbpoc/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-2.json
rename to src/mednet/config/data/tbpoc/fold-2.json
diff --git a/src/ptbench/config/data/tbpoc/fold-3.json b/src/mednet/config/data/tbpoc/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-3.json
rename to src/mednet/config/data/tbpoc/fold-3.json
diff --git a/src/ptbench/config/data/tbpoc/fold-4.json b/src/mednet/config/data/tbpoc/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-4.json
rename to src/mednet/config/data/tbpoc/fold-4.json
diff --git a/src/ptbench/config/data/tbpoc/fold-5.json b/src/mednet/config/data/tbpoc/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-5.json
rename to src/mednet/config/data/tbpoc/fold-5.json
diff --git a/src/ptbench/config/data/tbpoc/fold-6.json b/src/mednet/config/data/tbpoc/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-6.json
rename to src/mednet/config/data/tbpoc/fold-6.json
diff --git a/src/ptbench/config/data/tbpoc/fold-7.json b/src/mednet/config/data/tbpoc/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-7.json
rename to src/mednet/config/data/tbpoc/fold-7.json
diff --git a/src/ptbench/config/data/tbpoc/fold-8.json b/src/mednet/config/data/tbpoc/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-8.json
rename to src/mednet/config/data/tbpoc/fold-8.json
diff --git a/src/ptbench/config/data/tbpoc/fold-9.json b/src/mednet/config/data/tbpoc/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-9.json
rename to src/mednet/config/data/tbpoc/fold-9.json
diff --git a/src/ptbench/config/data/tbpoc/fold_0.py b/src/mednet/config/data/tbpoc/fold_0.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_0.py
rename to src/mednet/config/data/tbpoc/fold_0.py
index e3a0d242..03b5f6cd 100644
--- a/src/ptbench/config/data/tbpoc/fold_0.py
+++ b/src/mednet/config/data/tbpoc/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_1.py b/src/mednet/config/data/tbpoc/fold_1.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_1.py
rename to src/mednet/config/data/tbpoc/fold_1.py
index b6a04095..5db44367 100644
--- a/src/ptbench/config/data/tbpoc/fold_1.py
+++ b/src/mednet/config/data/tbpoc/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_2.py b/src/mednet/config/data/tbpoc/fold_2.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_2.py
rename to src/mednet/config/data/tbpoc/fold_2.py
index c821f0cc..5dea9179 100644
--- a/src/ptbench/config/data/tbpoc/fold_2.py
+++ b/src/mednet/config/data/tbpoc/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_3.py b/src/mednet/config/data/tbpoc/fold_3.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_3.py
rename to src/mednet/config/data/tbpoc/fold_3.py
index c5c9fa7d..bce854fc 100644
--- a/src/ptbench/config/data/tbpoc/fold_3.py
+++ b/src/mednet/config/data/tbpoc/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_4.py b/src/mednet/config/data/tbpoc/fold_4.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_4.py
rename to src/mednet/config/data/tbpoc/fold_4.py
index 9b3b74d9..55720bd3 100644
--- a/src/ptbench/config/data/tbpoc/fold_4.py
+++ b/src/mednet/config/data/tbpoc/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_5.py b/src/mednet/config/data/tbpoc/fold_5.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_5.py
rename to src/mednet/config/data/tbpoc/fold_5.py
index 7a9947dc..61bc52b5 100644
--- a/src/ptbench/config/data/tbpoc/fold_5.py
+++ b/src/mednet/config/data/tbpoc/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_6.py b/src/mednet/config/data/tbpoc/fold_6.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_6.py
rename to src/mednet/config/data/tbpoc/fold_6.py
index 0e6a7349..b7f166e6 100644
--- a/src/ptbench/config/data/tbpoc/fold_6.py
+++ b/src/mednet/config/data/tbpoc/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_7.py b/src/mednet/config/data/tbpoc/fold_7.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_7.py
rename to src/mednet/config/data/tbpoc/fold_7.py
index bb257c8e..3efab4a9 100644
--- a/src/ptbench/config/data/tbpoc/fold_7.py
+++ b/src/mednet/config/data/tbpoc/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_8.py b/src/mednet/config/data/tbpoc/fold_8.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_8.py
rename to src/mednet/config/data/tbpoc/fold_8.py
index 790f13c9..f23b85d5 100644
--- a/src/ptbench/config/data/tbpoc/fold_8.py
+++ b/src/mednet/config/data/tbpoc/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_9.py b/src/mednet/config/data/tbpoc/fold_9.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_9.py
rename to src/mednet/config/data/tbpoc/fold_9.py
index a53852a6..0391b39c 100644
--- a/src/ptbench/config/data/tbpoc/fold_9.py
+++ b/src/mednet/config/data/tbpoc/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/__init__.py b/src/mednet/config/data/tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/config/data/tbx11k/__init__.py
rename to src/mednet/config/data/tbx11k/__init__.py
diff --git a/src/ptbench/config/data/tbx11k/datamodule.py b/src/mednet/config/data/tbx11k/datamodule.py
similarity index 96%
rename from src/ptbench/config/data/tbx11k/datamodule.py
rename to src/mednet/config/data/tbx11k/datamodule.py
index 37ac5546..bd9156df 100644
--- a/src/ptbench/config/data/tbx11k/datamodule.py
+++ b/src/mednet/config/data/tbx11k/datamodule.py
@@ -10,12 +10,12 @@ import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/tbx11k/make_splits_from_database.py b/src/mednet/config/data/tbx11k/make_splits_from_database.py
similarity index 99%
rename from src/ptbench/config/data/tbx11k/make_splits_from_database.py
rename to src/mednet/config/data/tbx11k/make_splits_from_database.py
index 6584c251..c432a297 100644
--- a/src/ptbench/config/data/tbx11k/make_splits_from_database.py
+++ b/src/mednet/config/data/tbx11k/make_splits_from_database.py
@@ -2,7 +2,7 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""Converts TBX11k JSON annotation files into simplified JSON datasets for
-ptbench.
+mednet.
Requires ``datadir.tbx11k`` to be set on your configuration file, or that you
are sitting at the root directory of the database.
@@ -362,7 +362,7 @@ def main():
from clapper.rc import UserDefaults
datadir = pathlib.Path(
- UserDefaults("ptbench.toml").get(
+ UserDefaults("mednet.toml").get(
"datadir.tbx11k", os.path.realpath(os.curdir)
)
)
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-0.json b/src/mednet/config/data/tbx11k/v1-fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-0.json
rename to src/mednet/config/data/tbx11k/v1-fold-0.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-1.json b/src/mednet/config/data/tbx11k/v1-fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-1.json
rename to src/mednet/config/data/tbx11k/v1-fold-1.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-2.json b/src/mednet/config/data/tbx11k/v1-fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-2.json
rename to src/mednet/config/data/tbx11k/v1-fold-2.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-3.json b/src/mednet/config/data/tbx11k/v1-fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-3.json
rename to src/mednet/config/data/tbx11k/v1-fold-3.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-4.json b/src/mednet/config/data/tbx11k/v1-fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-4.json
rename to src/mednet/config/data/tbx11k/v1-fold-4.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-5.json b/src/mednet/config/data/tbx11k/v1-fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-5.json
rename to src/mednet/config/data/tbx11k/v1-fold-5.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-6.json b/src/mednet/config/data/tbx11k/v1-fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-6.json
rename to src/mednet/config/data/tbx11k/v1-fold-6.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-7.json b/src/mednet/config/data/tbx11k/v1-fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-7.json
rename to src/mednet/config/data/tbx11k/v1-fold-7.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-8.json b/src/mednet/config/data/tbx11k/v1-fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-8.json
rename to src/mednet/config/data/tbx11k/v1-fold-8.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-9.json b/src/mednet/config/data/tbx11k/v1-fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-9.json
rename to src/mednet/config/data/tbx11k/v1-fold-9.json
diff --git a/src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json b/src/mednet/config/data/tbx11k/v1-healthy-vs-atb.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json
rename to src/mednet/config/data/tbx11k/v1-healthy-vs-atb.json
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_0.py b/src/mednet/config/data/tbx11k/v1_fold_0.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_0.py
rename to src/mednet/config/data/tbx11k/v1_fold_0.py
index 9ba42d52..f2d5daa5 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_0.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_0.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-0.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_1.py b/src/mednet/config/data/tbx11k/v1_fold_1.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_1.py
rename to src/mednet/config/data/tbx11k/v1_fold_1.py
index ca3fe104..f137be59 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_1.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_1.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-1.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_2.py b/src/mednet/config/data/tbx11k/v1_fold_2.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_2.py
rename to src/mednet/config/data/tbx11k/v1_fold_2.py
index c3ec4fe4..cee8bcd2 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_2.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_2.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-2.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_3.py b/src/mednet/config/data/tbx11k/v1_fold_3.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_3.py
rename to src/mednet/config/data/tbx11k/v1_fold_3.py
index 09fb16b2..5527c47a 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_3.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_3.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-3.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_4.py b/src/mednet/config/data/tbx11k/v1_fold_4.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_4.py
rename to src/mednet/config/data/tbx11k/v1_fold_4.py
index 8f96d1e5..800239d5 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_4.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_4.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-4.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_5.py b/src/mednet/config/data/tbx11k/v1_fold_5.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_5.py
rename to src/mednet/config/data/tbx11k/v1_fold_5.py
index 8ced06d4..e0ca7876 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_5.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_5.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-5.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_6.py b/src/mednet/config/data/tbx11k/v1_fold_6.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_6.py
rename to src/mednet/config/data/tbx11k/v1_fold_6.py
index 28e9f16a..79ba3cd5 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_6.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_6.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-6.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_7.py b/src/mednet/config/data/tbx11k/v1_fold_7.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_7.py
rename to src/mednet/config/data/tbx11k/v1_fold_7.py
index 09886b94..e873f858 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_7.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_7.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-7.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_8.py b/src/mednet/config/data/tbx11k/v1_fold_8.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_8.py
rename to src/mednet/config/data/tbx11k/v1_fold_8.py
index 5fd2dd23..21aea93e 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_8.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_8.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-8.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_9.py b/src/mednet/config/data/tbx11k/v1_fold_9.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_9.py
rename to src/mednet/config/data/tbx11k/v1_fold_9.py
index 440f724f..47e0ae33 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_9.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_9.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py b/src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
similarity index 82%
rename from src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
rename to src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
index 785b6bfb..b97d7a52 100644
--- a/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
+++ b/src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
@@ -27,10 +27,10 @@ Split v1 contains healthy subjects against active TB cases (total samples =
- Active TB only: 157
- Total: 957
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-healthy-vs-atb.json")
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-0.json b/src/mednet/config/data/tbx11k/v2-fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-0.json
rename to src/mednet/config/data/tbx11k/v2-fold-0.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-1.json b/src/mednet/config/data/tbx11k/v2-fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-1.json
rename to src/mednet/config/data/tbx11k/v2-fold-1.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-2.json b/src/mednet/config/data/tbx11k/v2-fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-2.json
rename to src/mednet/config/data/tbx11k/v2-fold-2.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-3.json b/src/mednet/config/data/tbx11k/v2-fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-3.json
rename to src/mednet/config/data/tbx11k/v2-fold-3.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-4.json b/src/mednet/config/data/tbx11k/v2-fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-4.json
rename to src/mednet/config/data/tbx11k/v2-fold-4.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-5.json b/src/mednet/config/data/tbx11k/v2-fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-5.json
rename to src/mednet/config/data/tbx11k/v2-fold-5.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-6.json b/src/mednet/config/data/tbx11k/v2-fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-6.json
rename to src/mednet/config/data/tbx11k/v2-fold-6.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-7.json b/src/mednet/config/data/tbx11k/v2-fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-7.json
rename to src/mednet/config/data/tbx11k/v2-fold-7.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-8.json b/src/mednet/config/data/tbx11k/v2-fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-8.json
rename to src/mednet/config/data/tbx11k/v2-fold-8.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-9.json b/src/mednet/config/data/tbx11k/v2-fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-9.json
rename to src/mednet/config/data/tbx11k/v2-fold-9.json
diff --git a/src/ptbench/config/data/tbx11k/v2-others-vs-atb.json b/src/mednet/config/data/tbx11k/v2-others-vs-atb.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-others-vs-atb.json
rename to src/mednet/config/data/tbx11k/v2-others-vs-atb.json
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_0.py b/src/mednet/config/data/tbx11k/v2_fold_0.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_0.py
rename to src/mednet/config/data/tbx11k/v2_fold_0.py
index c713c479..565bc706 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_0.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_0.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-0.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_1.py b/src/mednet/config/data/tbx11k/v2_fold_1.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_1.py
rename to src/mednet/config/data/tbx11k/v2_fold_1.py
index 10b3b183..77d73704 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_1.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_1.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-1.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_2.py b/src/mednet/config/data/tbx11k/v2_fold_2.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_2.py
rename to src/mednet/config/data/tbx11k/v2_fold_2.py
index f7fd10a6..eac8cb9a 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_2.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_2.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-2.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_3.py b/src/mednet/config/data/tbx11k/v2_fold_3.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_3.py
rename to src/mednet/config/data/tbx11k/v2_fold_3.py
index b744251d..ec0de165 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_3.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_3.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-3.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_4.py b/src/mednet/config/data/tbx11k/v2_fold_4.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_4.py
rename to src/mednet/config/data/tbx11k/v2_fold_4.py
index 17215495..f3491d51 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_4.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_4.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-4.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_5.py b/src/mednet/config/data/tbx11k/v2_fold_5.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_5.py
rename to src/mednet/config/data/tbx11k/v2_fold_5.py
index 41a5ba43..9cb818a4 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_5.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_5.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-5.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_6.py b/src/mednet/config/data/tbx11k/v2_fold_6.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_6.py
rename to src/mednet/config/data/tbx11k/v2_fold_6.py
index 0f82163d..15014857 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_6.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_6.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-6.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_7.py b/src/mednet/config/data/tbx11k/v2_fold_7.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_7.py
rename to src/mednet/config/data/tbx11k/v2_fold_7.py
index 6f3d958b..c3a63f6c 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_7.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_7.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-7.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_8.py b/src/mednet/config/data/tbx11k/v2_fold_8.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_8.py
rename to src/mednet/config/data/tbx11k/v2_fold_8.py
index 3b10a652..0a4f348e 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_8.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_8.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-8.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_9.py b/src/mednet/config/data/tbx11k/v2_fold_9.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_9.py
rename to src/mednet/config/data/tbx11k/v2_fold_9.py
index 86922305..2c087bd4 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_9.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_9.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py b/src/mednet/config/data/tbx11k/v2_others_vs_atb.py
similarity index 84%
rename from src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
rename to src/mednet/config/data/tbx11k/v2_others_vs_atb.py
index a5e8c480..5f50e19d 100644
--- a/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
+++ b/src/mednet/config/data/tbx11k/v2_others_vs_atb.py
@@ -27,10 +27,10 @@ active TB cases (total samples = 8369):
- Active TB only: 157
- Total: 1793
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-others-vs-atb.json")
diff --git a/src/ptbench/config/models/__init__.py b/src/mednet/config/models/__init__.py
similarity index 100%
rename from src/ptbench/config/models/__init__.py
rename to src/mednet/config/models/__init__.py
diff --git a/src/ptbench/config/models/alexnet.py b/src/mednet/config/models/alexnet.py
similarity index 86%
rename from src/ptbench/config/models/alexnet.py
rename to src/mednet/config/models/alexnet.py
index fce6ba64..9703f964 100644
--- a/src/ptbench/config/models/alexnet.py
+++ b/src/mednet/config/models/alexnet.py
@@ -11,8 +11,8 @@ page <alexnet-pytorch_>`_), modified for a variable number of outputs
from torch.nn import BCEWithLogitsLoss
from torch.optim import SGD
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.alexnet import Alexnet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.alexnet import Alexnet
model = Alexnet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/alexnet_pretrained.py b/src/mednet/config/models/alexnet_pretrained.py
similarity index 87%
rename from src/ptbench/config/models/alexnet_pretrained.py
rename to src/mednet/config/models/alexnet_pretrained.py
index 81f72b87..8887db8f 100644
--- a/src/ptbench/config/models/alexnet_pretrained.py
+++ b/src/mednet/config/models/alexnet_pretrained.py
@@ -13,8 +13,8 @@ N.B.: The output layer is **always** initialized from scratch.
from torch.nn import BCEWithLogitsLoss
from torch.optim import SGD
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.alexnet import Alexnet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.alexnet import Alexnet
model = Alexnet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet.py b/src/mednet/config/models/densenet.py
similarity index 86%
rename from src/ptbench/config/models/densenet.py
rename to src/mednet/config/models/densenet.py
index bfee577f..9fbf388d 100644
--- a/src/ptbench/config/models/densenet.py
+++ b/src/mednet/config/models/densenet.py
@@ -11,8 +11,8 @@ page <densenet_pytorch_>`), modified for a variable number of outputs
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet_pretrained.py b/src/mednet/config/models/densenet_pretrained.py
similarity index 87%
rename from src/ptbench/config/models/densenet_pretrained.py
rename to src/mednet/config/models/densenet_pretrained.py
index 9b1fa4ca..7d85d9b4 100644
--- a/src/ptbench/config/models/densenet_pretrained.py
+++ b/src/mednet/config/models/densenet_pretrained.py
@@ -13,8 +13,8 @@ N.B.: The output layer is **always** initialized from scratch.
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet_rs.py b/src/mednet/config/models/densenet_rs.py
similarity index 88%
rename from src/ptbench/config/models/densenet_rs.py
rename to src/mednet/config/models/densenet_rs.py
index 3f625686..24caef86 100644
--- a/src/ptbench/config/models/densenet_rs.py
+++ b/src/mednet/config/models/densenet_rs.py
@@ -12,8 +12,8 @@ weights from scratch for radiological sign detection.
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/logistic_regression.py b/src/mednet/config/models/logistic_regression.py
similarity index 86%
rename from src/ptbench/config/models/logistic_regression.py
rename to src/mednet/config/models/logistic_regression.py
index b93589df..bd327ed4 100644
--- a/src/ptbench/config/models/logistic_regression.py
+++ b/src/mednet/config/models/logistic_regression.py
@@ -8,6 +8,6 @@ the output of :py:mod:`.densenet_rs` and be trained for binary classification
(e.g. for active TB detection).
"""
-from ptbench.models.logistic_regression import LogisticRegression
+from mednet.models.logistic_regression import LogisticRegression
model = LogisticRegression(input_size=14)
diff --git a/src/ptbench/config/models/mlp.py b/src/mednet/config/models/mlp.py
similarity index 87%
rename from src/ptbench/config/models/mlp.py
rename to src/mednet/config/models/mlp.py
index c87432d7..4791a840 100644
--- a/src/ptbench/config/models/mlp.py
+++ b/src/mednet/config/models/mlp.py
@@ -8,6 +8,6 @@ output (e.g. to predict active TB presence from radiological finding
estimates).
"""
-from ptbench.models.mlp import MultiLayerPerceptron
+from mednet.models.mlp import MultiLayerPerceptron
model = MultiLayerPerceptron()
diff --git a/src/ptbench/config/models/pasa.py b/src/mednet/config/models/pasa.py
similarity index 88%
rename from src/ptbench/config/models/pasa.py
rename to src/mednet/config/models/pasa.py
index c419b5fe..227b9b42 100644
--- a/src/ptbench/config/models/pasa.py
+++ b/src/mednet/config/models/pasa.py
@@ -13,8 +13,8 @@ Reference: [PASA-2019]_
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.pasa import Pasa
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.pasa import Pasa
model = Pasa(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/data/__init__.py b/src/mednet/data/__init__.py
similarity index 100%
rename from src/ptbench/data/__init__.py
rename to src/mednet/data/__init__.py
diff --git a/src/ptbench/data/augmentations.py b/src/mednet/data/augmentations.py
similarity index 100%
rename from src/ptbench/data/augmentations.py
rename to src/mednet/data/augmentations.py
diff --git a/src/ptbench/data/datamodule.py b/src/mednet/data/datamodule.py
similarity index 100%
rename from src/ptbench/data/datamodule.py
rename to src/mednet/data/datamodule.py
diff --git a/src/ptbench/data/image_utils.py b/src/mednet/data/image_utils.py
similarity index 100%
rename from src/ptbench/data/image_utils.py
rename to src/mednet/data/image_utils.py
diff --git a/src/ptbench/data/split.py b/src/mednet/data/split.py
similarity index 100%
rename from src/ptbench/data/split.py
rename to src/mednet/data/split.py
diff --git a/src/ptbench/data/typing.py b/src/mednet/data/typing.py
similarity index 100%
rename from src/ptbench/data/typing.py
rename to src/mednet/data/typing.py
diff --git a/src/ptbench/engine/__init__.py b/src/mednet/engine/__init__.py
similarity index 100%
rename from src/ptbench/engine/__init__.py
rename to src/mednet/engine/__init__.py
diff --git a/src/ptbench/engine/callbacks.py b/src/mednet/engine/callbacks.py
similarity index 100%
rename from src/ptbench/engine/callbacks.py
rename to src/mednet/engine/callbacks.py
diff --git a/src/ptbench/engine/device.py b/src/mednet/engine/device.py
similarity index 100%
rename from src/ptbench/engine/device.py
rename to src/mednet/engine/device.py
diff --git a/src/ptbench/engine/evaluator.py b/src/mednet/engine/evaluator.py
similarity index 100%
rename from src/ptbench/engine/evaluator.py
rename to src/mednet/engine/evaluator.py
diff --git a/src/ptbench/engine/loggers.py b/src/mednet/engine/loggers.py
similarity index 100%
rename from src/ptbench/engine/loggers.py
rename to src/mednet/engine/loggers.py
diff --git a/src/ptbench/engine/predictor.py b/src/mednet/engine/predictor.py
similarity index 100%
rename from src/ptbench/engine/predictor.py
rename to src/mednet/engine/predictor.py
diff --git a/src/ptbench/engine/trainer.py b/src/mednet/engine/trainer.py
similarity index 100%
rename from src/ptbench/engine/trainer.py
rename to src/mednet/engine/trainer.py
diff --git a/src/ptbench/models/__init__.py b/src/mednet/models/__init__.py
similarity index 100%
rename from src/ptbench/models/__init__.py
rename to src/mednet/models/__init__.py
diff --git a/src/ptbench/models/alexnet.py b/src/mednet/models/alexnet.py
similarity index 100%
rename from src/ptbench/models/alexnet.py
rename to src/mednet/models/alexnet.py
diff --git a/src/ptbench/models/densenet.py b/src/mednet/models/densenet.py
similarity index 100%
rename from src/ptbench/models/densenet.py
rename to src/mednet/models/densenet.py
diff --git a/src/ptbench/models/logistic_regression.py b/src/mednet/models/logistic_regression.py
similarity index 100%
rename from src/ptbench/models/logistic_regression.py
rename to src/mednet/models/logistic_regression.py
diff --git a/src/ptbench/models/loss_weights.py b/src/mednet/models/loss_weights.py
similarity index 100%
rename from src/ptbench/models/loss_weights.py
rename to src/mednet/models/loss_weights.py
diff --git a/src/ptbench/models/mlp.py b/src/mednet/models/mlp.py
similarity index 100%
rename from src/ptbench/models/mlp.py
rename to src/mednet/models/mlp.py
diff --git a/src/ptbench/models/normalizer.py b/src/mednet/models/normalizer.py
similarity index 100%
rename from src/ptbench/models/normalizer.py
rename to src/mednet/models/normalizer.py
diff --git a/src/ptbench/models/pasa.py b/src/mednet/models/pasa.py
similarity index 100%
rename from src/ptbench/models/pasa.py
rename to src/mednet/models/pasa.py
diff --git a/src/ptbench/models/separate.py b/src/mednet/models/separate.py
similarity index 100%
rename from src/ptbench/models/separate.py
rename to src/mednet/models/separate.py
diff --git a/src/ptbench/models/transforms.py b/src/mednet/models/transforms.py
similarity index 100%
rename from src/ptbench/models/transforms.py
rename to src/mednet/models/transforms.py
diff --git a/src/ptbench/models/typing.py b/src/mednet/models/typing.py
similarity index 100%
rename from src/ptbench/models/typing.py
rename to src/mednet/models/typing.py
diff --git a/src/ptbench/scripts/__init__.py b/src/mednet/scripts/__init__.py
similarity index 100%
rename from src/ptbench/scripts/__init__.py
rename to src/mednet/scripts/__init__.py
diff --git a/src/ptbench/scripts/cli.py b/src/mednet/scripts/cli.py
similarity index 100%
rename from src/ptbench/scripts/cli.py
rename to src/mednet/scripts/cli.py
diff --git a/src/ptbench/scripts/click.py b/src/mednet/scripts/click.py
similarity index 100%
rename from src/ptbench/scripts/click.py
rename to src/mednet/scripts/click.py
diff --git a/src/ptbench/scripts/config.py b/src/mednet/scripts/config.py
similarity index 92%
rename from src/ptbench/scripts/config.py
rename to src/mednet/scripts/config.py
index d8c105c5..14abfe9a 100644
--- a/src/ptbench/scripts/config.py
+++ b/src/mednet/scripts/config.py
@@ -24,11 +24,11 @@ def config():
epilog="""Examples:
\b
- 1. Lists all configuration resources (type: ptbench.config) installed:
+ 1. Lists all configuration resources (type: mednet.config) installed:
.. code:: sh
- ptbench config list
+ mednet config list
\b
@@ -37,7 +37,7 @@ def config():
.. code:: sh
- ptbench config list -v
+ mednet config list -v
"""
)
@@ -45,7 +45,7 @@ def config():
def list(verbose) -> None:
"""Lists configuration files installed."""
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
@@ -102,7 +102,7 @@ def list(verbose) -> None:
.. code:: sh
- ptbench config describe montgomery
+ mednet config describe montgomery
\b
@@ -111,7 +111,7 @@ def list(verbose) -> None:
.. code:: sh
- ptbench config describe montgomery -v
+ mednet config describe montgomery -v
"""
)
@@ -124,7 +124,7 @@ def list(verbose) -> None:
def describe(name, verbose) -> None:
"""Describes a specific configuration file."""
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
@@ -157,7 +157,7 @@ def describe(name, verbose) -> None:
.. code:: sh
- $ ptbench config copy montgomery -vvv newdataset.py
+ $ mednet config copy montgomery -vvv newdataset.py
"""
)
@@ -177,7 +177,7 @@ def copy(source, destination) -> None:
import shutil
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
diff --git a/src/ptbench/scripts/database.py b/src/mednet/scripts/database.py
similarity index 95%
rename from src/ptbench/scripts/database.py
rename to src/mednet/scripts/database.py
index c99f465a..683cad2e 100644
--- a/src/ptbench/scripts/database.py
+++ b/src/mednet/scripts/database.py
@@ -20,7 +20,7 @@ def _get_raw_databases() -> dict[str, dict[str, str]]:
containing two string keys:
* ``module``: the full Pythonic module name (e.g.
- ``ptbench.data.montgomery``)
+ ``mednet.data.montgomery``)
* ``datadir``: points to the user-configured data directory for the
current dataset, if set, or ``None`` otherwise.
"""
@@ -68,7 +68,7 @@ def database() -> None:
1. To install a database, set up its data directory ("datadir"). For
example, to setup access to Montgomery files you downloaded locally at
the directory "/path/to/montgomery/files", edit the RC file (typically
- ``$HOME/.config/ptbench.toml``), and add a line like the following:
+ ``$HOME/.config/mednet.toml``), and add a line like the following:
.. code:: toml
@@ -84,7 +84,7 @@ def database() -> None:
.. code:: sh
- $ ptbench database list
+ $ mednet database list
""",
)
@@ -113,7 +113,7 @@ def list():
.. code:: sh
- ptbench datamodule check -vv montgomery-f0
+ mednet datamodule check -vv montgomery-f0
""",
)
@@ -138,7 +138,7 @@ def check(split, limit):
click.secho(f"Checking split `{split}`...", fg="yellow")
try:
- module = importlib.metadata.entry_points(group="ptbench.config")[
+ module = importlib.metadata.entry_points(group="mednet.config")[
split
].module
except KeyError:
diff --git a/src/ptbench/scripts/evaluate.py b/src/mednet/scripts/evaluate.py
similarity index 95%
rename from src/ptbench/scripts/evaluate.py
rename to src/mednet/scripts/evaluate.py
index 2e4fe626..e2dab699 100644
--- a/src/ptbench/scripts/evaluate.py
+++ b/src/mednet/scripts/evaluate.py
@@ -18,7 +18,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -26,13 +26,13 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- ptbench evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results
+ mednet evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results
2. Runs evaluation on an existing prediction output, tune threshold a priori on the `validation` set:
.. code:: sh
- ptbench evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results --threshold=validation
+ mednet evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results --threshold=validation
""",
)
@click.option(
diff --git a/src/ptbench/scripts/experiment.py b/src/mednet/scripts/experiment.py
similarity index 97%
rename from src/ptbench/scripts/experiment.py
rename to src/mednet/scripts/experiment.py
index 55c24260..550eb56f 100644
--- a/src/ptbench/scripts/experiment.py
+++ b/src/mednet/scripts/experiment.py
@@ -16,7 +16,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -27,7 +27,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- $ ptbench experiment -vv pasa montgomery --epochs=2
+ $ mednet experiment -vv pasa montgomery --epochs=2
""",
)
@training_options
diff --git a/src/ptbench/scripts/predict.py b/src/mednet/scripts/predict.py
similarity index 94%
rename from src/ptbench/scripts/predict.py
rename to src/mednet/scripts/predict.py
index 91b66d72..f69f7321 100644
--- a/src/ptbench/scripts/predict.py
+++ b/src/mednet/scripts/predict.py
@@ -15,7 +15,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -23,13 +23,13 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- ptbench predict -vv pasa montgomery --weight=path/to/model.ckpt --output=path/to/predictions.json
+ mednet predict -vv pasa montgomery --weight=path/to/model.ckpt --output=path/to/predictions.json
2. Enables multi-processing data loading with 6 processes:
.. code:: sh
- ptbench predict -vv pasa montgomery --parallel=6 --weight=path/to/model.ckpt --output=path/to/predictions.json
+ mednet predict -vv pasa montgomery --parallel=6 --weight=path/to/model.ckpt --output=path/to/predictions.json
""",
)
diff --git a/src/ptbench/scripts/train.py b/src/mednet/scripts/train.py
similarity index 99%
rename from src/ptbench/scripts/train.py
rename to src/mednet/scripts/train.py
index 8dcd832a..36d6efb3 100644
--- a/src/ptbench/scripts/train.py
+++ b/src/mednet/scripts/train.py
@@ -222,7 +222,7 @@ def reusable_options(f):
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -230,7 +230,7 @@ def reusable_options(f):
.. code:: sh
- ptbench train -vv pasa montgomery --batch-size=4 --device="cuda:0"
+ mednet train -vv pasa montgomery --batch-size=4 --device="cuda:0"
""",
)
@reusable_options
diff --git a/src/ptbench/scripts/train_analysis.py b/src/mednet/scripts/train_analysis.py
similarity index 98%
rename from src/ptbench/scripts/train_analysis.py
rename to src/mednet/scripts/train_analysis.py
index f108f00d..94867b6a 100644
--- a/src/ptbench/scripts/train_analysis.py
+++ b/src/mednet/scripts/train_analysis.py
@@ -113,7 +113,7 @@ def create_figures(
.. code:: sh
- ptbench train-analysis -vv results/logs
+ mednet train-analysis -vv results/logs
""",
)
@click.argument(
diff --git a/src/ptbench/scripts/utils.py b/src/mednet/scripts/utils.py
similarity index 100%
rename from src/ptbench/scripts/utils.py
rename to src/mednet/scripts/utils.py
diff --git a/src/ptbench/utils/__init__.py b/src/mednet/utils/__init__.py
similarity index 100%
rename from src/ptbench/utils/__init__.py
rename to src/mednet/utils/__init__.py
diff --git a/src/ptbench/utils/checkpointer.py b/src/mednet/utils/checkpointer.py
similarity index 100%
rename from src/ptbench/utils/checkpointer.py
rename to src/mednet/utils/checkpointer.py
diff --git a/src/ptbench/utils/rc.py b/src/mednet/utils/rc.py
similarity index 86%
rename from src/ptbench/utils/rc.py
rename to src/mednet/utils/rc.py
index 21ebda08..1a99df49 100644
--- a/src/ptbench/utils/rc.py
+++ b/src/mednet/utils/rc.py
@@ -7,4 +7,4 @@ from clapper.rc import UserDefaults
def load_rc() -> UserDefaults:
"""Returns global configuration variables."""
- return UserDefaults("ptbench.toml")
+ return UserDefaults("mednet.toml")
diff --git a/src/ptbench/utils/resources.py b/src/mednet/utils/resources.py
similarity index 100%
rename from src/ptbench/utils/resources.py
rename to src/mednet/utils/resources.py
diff --git a/src/ptbench/utils/summary.py b/src/mednet/utils/summary.py
similarity index 100%
rename from src/ptbench/utils/summary.py
rename to src/mednet/utils/summary.py
diff --git a/src/ptbench/utils/tensorboard.py b/src/mednet/utils/tensorboard.py
similarity index 100%
rename from src/ptbench/utils/tensorboard.py
rename to src/mednet/utils/tensorboard.py
diff --git a/tests/conftest.py b/tests/conftest.py
index 82eef644..60d00e28 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -12,7 +12,7 @@ import pytest
import tomli_w
import torch
-from ptbench.data.typing import DatabaseSplit
+from mednet.data.typing import DatabaseSplit
@pytest.fixture
@@ -26,7 +26,7 @@ def pytest_configure(config):
config.addinivalue_line(
"markers",
"skip_if_rc_var_not_set(name): this mark skips the test if a certain "
- "~/.config/ptbench.toml variable is not set",
+ "~/.config/mednet.toml variable is not set",
)
config.addinivalue_line("markers", "slow: this mark indicates slow tests")
@@ -38,7 +38,7 @@ def pytest_runtest_setup(item):
The test is run if this function returns ``None``. To skip a test,
call ``pytest.skip()``, specifying a reason.
"""
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
@@ -49,19 +49,19 @@ def pytest_runtest_setup(item):
for mark in item.iter_markers(name="skip_if_rc_var_not_set")
]
- # checks all names mentioned are set in ~/.config/ptbench.toml, otherwise,
+ # checks all names mentioned are set in ~/.config/mednet.toml, otherwise,
# skip the test
if rc_names:
missing = [k for k in rc_names if rc.get(k) is None]
if any(missing):
pytest.skip(
f"Test skipped because {', '.join(missing)} is **not** "
- f"set in ~/.config/ptbench.toml"
+ f"set in ~/.config/mednet.toml"
)
def rc_variable_set(name):
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
pytest.mark.skipif(
@@ -79,7 +79,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
"""Presets the session start to ensure the Montgomery dataset is always
available."""
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
@@ -94,7 +94,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
)
assert archive.exists(), (
f"Neither datadir.montgomery is set on the global configuration, "
- f"(typically ~/.config/ptbench.toml), or it is possible to detect "
+ f"(typically ~/.config/mednet.toml), or it is possible to detect "
f"the presence of {archive}' (did you git submodule init --update "
f"this submodule?)"
)
@@ -105,7 +105,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
with zipfile.ZipFile(archive) as zf:
zf.extractall(montgomery_tempdir.name)
- config_filename = "ptbench.toml"
+ config_filename = "mednet.toml"
with open(
os.path.join(montgomery_tempdir.name, config_filename), "wb"
) as f:
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 5799e332..da377d38 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -24,7 +24,7 @@ def stdout_logging():
ch = logging.StreamHandler(buf)
ch.setFormatter(logging.Formatter("%(message)s"))
ch.setLevel(logging.INFO)
- logger = logging.getLogger("ptbench")
+ logger = logging.getLogger("mednet")
logger.addHandler(ch)
yield buf
logger.removeHandler(ch)
@@ -44,45 +44,45 @@ def _check_help(entry_point):
def test_config_help():
- from ptbench.scripts.config import config
+ from mednet.scripts.config import config
_check_help(config)
def test_config_list_help():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
_check_help(list)
def test_config_list():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
runner = CliRunner()
result = runner.invoke(list)
_assert_exit_0(result)
- assert "module: ptbench.config.data" in result.output
- assert "module: ptbench.config.models" in result.output
+ assert "module: mednet.config.data" in result.output
+ assert "module: mednet.config.models" in result.output
def test_config_list_v():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
result = CliRunner().invoke(list, ["--verbose"])
_assert_exit_0(result)
- assert "module: ptbench.config.data" in result.output
- assert "module: ptbench.config.models" in result.output
+ assert "module: mednet.config.data" in result.output
+ assert "module: mednet.config.models" in result.output
def test_config_describe_help():
- from ptbench.scripts.config import describe
+ from mednet.scripts.config import describe
_check_help(describe)
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_config_describe_montgomery():
- from ptbench.scripts.config import describe
+ from mednet.scripts.config import describe
runner = CliRunner()
result = runner.invoke(describe, ["montgomery"])
@@ -91,19 +91,19 @@ def test_config_describe_montgomery():
def test_database_help():
- from ptbench.scripts.database import database
+ from mednet.scripts.database import database
_check_help(database)
def test_datamodule_list_help():
- from ptbench.scripts.database import list
+ from mednet.scripts.database import list
_check_help(list)
def test_datamodule_list():
- from ptbench.scripts.database import list
+ from mednet.scripts.database import list
runner = CliRunner()
result = runner.invoke(list)
@@ -112,14 +112,14 @@ def test_datamodule_list():
def test_datamodule_check_help():
- from ptbench.scripts.database import check
+ from mednet.scripts.database import check
_check_help(check)
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_database_check():
- from ptbench.scripts.database import check
+ from mednet.scripts.database import check
runner = CliRunner()
result = runner.invoke(check, ["--verbose", "--limit=1", "montgomery"])
@@ -127,13 +127,13 @@ def test_database_check():
def test_main_help():
- from ptbench.scripts.cli import cli
+ from mednet.scripts.cli import cli
_check_help(cli)
def test_train_help():
- from ptbench.scripts.train import train
+ from mednet.scripts.train import train
_check_help(train)
@@ -143,20 +143,20 @@ def _str_counter(substr, s):
def test_predict_help():
- from ptbench.scripts.predict import predict
+ from mednet.scripts.predict import predict
_check_help(predict)
def test_evaluate_help():
- from ptbench.scripts.evaluate import evaluate
+ from mednet.scripts.evaluate import evaluate
_check_help(evaluate)
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery(temporary_basedir):
- from ptbench.scripts.train import train
+ from mednet.scripts.train import train
runner = CliRunner()
@@ -217,7 +217,7 @@ def test_train_pasa_montgomery(temporary_basedir):
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
- from ptbench.scripts.train import train
+ from mednet.scripts.train import train
runner = CliRunner()
@@ -311,7 +311,7 @@ def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
# @pytest.mark.skip(reason="Test need to be updated")
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_predict_pasa_montgomery(temporary_basedir, datadir):
- from ptbench.scripts.predict import predict
+ from mednet.scripts.predict import predict
runner = CliRunner()
@@ -356,7 +356,7 @@ def test_predict_pasa_montgomery(temporary_basedir, datadir):
# @pytest.mark.skip(reason="Test need to be updated")
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_evaluate_pasa_montgomery(temporary_basedir):
- from ptbench.scripts.evaluate import evaluate
+ from mednet.scripts.evaluate import evaluate
runner = CliRunner()
@@ -401,7 +401,7 @@ def test_evaluate_pasa_montgomery(temporary_basedir):
# @pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
# def test_predict_densenetrs_montgomery(temporary_basedir, datadir):
-# from ptbench.scripts.predict import predict
+# from mednet.scripts.predict import predict
# runner = CliRunner()
diff --git a/tests/test_database_split.py b/tests/test_database_split.py
index aa360e2c..f7d8d340 100644
--- a/tests/test_database_split.py
+++ b/tests/test_database_split.py
@@ -3,7 +3,7 @@
# SPDX-License-Identifier: GPL-3.0-or-later
"""Test code for datasets."""
-from ptbench.data.split import CSVDatabaseSplit, JSONDatabaseSplit
+from mednet.data.split import CSVDatabaseSplit, JSONDatabaseSplit
def test_csv_loading(datadir):
diff --git a/tests/test_evaluator.py b/tests/test_evaluator.py
index 5394dc6f..1fc4ae63 100644
--- a/tests/test_evaluator.py
+++ b/tests/test_evaluator.py
@@ -7,7 +7,7 @@ import numpy
def test_centered_maxf1():
- from ptbench.engine.evaluator import _get_centered_maxf1
+ from mednet.engine.evaluator import _get_centered_maxf1
# Multiple max F1
f1_scores = numpy.array([0.8, 0.9, 1.0, 1.0, 1.0, 0.3])
diff --git a/tests/test_hivtb.py b/tests/test_hivtb.py
index 13119812..00b7a484 100644
--- a/tests/test_hivtb.py
+++ b/tests/test_hivtb.py
@@ -33,7 +33,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.hivtb.datamodule import make_split
+ from mednet.config.data.hivtb.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -69,7 +69,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.hivtb"
+ f".{name}", "mednet.config.data.hivtb"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_image_utils.py b/tests/test_image_utils.py
index 420fdf04..57317c22 100644
--- a/tests/test_image_utils.py
+++ b/tests/test_image_utils.py
@@ -6,7 +6,7 @@
import numpy
import PIL.Image
-from ptbench.data.image_utils import remove_black_borders
+from mednet.data.image_utils import remove_black_borders
def test_remove_black_borders(datadir):
diff --git a/tests/test_indian.py b/tests/test_indian.py
index e86b56f6..66ffdef3 100644
--- a/tests/test_indian.py
+++ b/tests/test_indian.py
@@ -37,7 +37,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.indian.datamodule import make_split
+ from mednet.config.data.indian.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -74,7 +74,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_montgomery.py b/tests/test_montgomery.py
index 1e8227d3..6933e982 100644
--- a/tests/test_montgomery.py
+++ b/tests/test_montgomery.py
@@ -34,7 +34,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.montgomery.datamodule import make_split
+ from mednet.config.data.montgomery.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -71,7 +71,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_montgomery_shenzhen.py b/tests/test_montgomery_shenzhen.py
index 9af425a5..7f711905 100644
--- a/tests/test_montgomery_shenzhen.py
+++ b/tests/test_montgomery_shenzhen.py
@@ -26,23 +26,23 @@ import pytest
)
def test_split_consistency(name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen"
+ f".{name}", "mednet.config.data.montgomery_shenzhen"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian.py b/tests/test_montgomery_shenzhen_indian.py
index b3c7f5f5..3134574e 100644
--- a/tests/test_montgomery_shenzhen_indian.py
+++ b/tests/test_montgomery_shenzhen_indian.py
@@ -26,31 +26,31 @@ import pytest
)
def test_split_consistency(name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen_indian"
+ f".{name}", "mednet.config.data.montgomery_shenzhen_indian"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian_padchest.py b/tests/test_montgomery_shenzhen_indian_padchest.py
index 95b59bf1..84b0aca9 100644
--- a/tests/test_montgomery_shenzhen_indian_padchest.py
+++ b/tests/test_montgomery_shenzhen_indian_padchest.py
@@ -16,39 +16,39 @@ import pytest
)
def test_split_consistency(name: str, padchest_name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.config.data.padchest"
+ f".{padchest_name}", "mednet.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen_indian_padchest"
+ f".{name}", "mednet.config.data.montgomery_shenzhen_indian_padchest"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.padchest"
+ ".datamodule", "mednet.config.data.padchest"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian_tbx11k.py b/tests/test_montgomery_shenzhen_indian_tbx11k.py
index 71956b49..d38cd77a 100644
--- a/tests/test_montgomery_shenzhen_indian_tbx11k.py
+++ b/tests/test_montgomery_shenzhen_indian_tbx11k.py
@@ -37,40 +37,40 @@ import pytest
)
def test_split_consistency(name: str, tbx11k_name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
tbx11k = importlib.import_module(
- f".{tbx11k_name}", "ptbench.config.data.tbx11k"
+ f".{tbx11k_name}", "mednet.config.data.tbx11k"
).datamodule
combined = importlib.import_module(
f".{tbx11k_name}",
- "ptbench.config.data.montgomery_shenzhen_indian_tbx11k",
+ "mednet.config.data.montgomery_shenzhen_indian_tbx11k",
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
TBX11kLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.tbx11k"
+ ".datamodule", "mednet.config.data.tbx11k"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_nih_cxr14.py b/tests/test_nih_cxr14.py
index 83f45212..8188c7cb 100644
--- a/tests/test_nih_cxr14.py
+++ b/tests/test_nih_cxr14.py
@@ -25,7 +25,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.nih_cxr14.datamodule import make_split
+ from mednet.config.data.nih_cxr14.datamodule import make_split
database_checkers.check_split(
make_split(split),
@@ -52,7 +52,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.nih_cxr14"
+ f".{name}", "mednet.config.data.nih_cxr14"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_nih_cxr14_padchest.py b/tests/test_nih_cxr14_padchest.py
index 5c5bb5ef..2c013398 100644
--- a/tests/test_nih_cxr14_padchest.py
+++ b/tests/test_nih_cxr14_padchest.py
@@ -16,23 +16,23 @@ import pytest
)
def test_split_consistency(name: str, padchest_name: str, combined_name: str):
nih_cxr14 = importlib.import_module(
- f".{name}", "ptbench.config.data.nih_cxr14"
+ f".{name}", "mednet.config.data.nih_cxr14"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.config.data.padchest"
+ f".{padchest_name}", "mednet.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{combined_name}", "ptbench.config.data.nih_cxr14_padchest"
+ f".{combined_name}", "mednet.config.data.nih_cxr14_padchest"
).datamodule
CXR14Loader = importlib.import_module(
- ".datamodule", "ptbench.config.data.nih_cxr14"
+ ".datamodule", "mednet.config.data.nih_cxr14"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.padchest"
+ ".datamodule", "mednet.config.data.padchest"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_padchest.py b/tests/test_padchest.py
index 54b42b6d..dfa491c8 100644
--- a/tests/test_padchest.py
+++ b/tests/test_padchest.py
@@ -30,7 +30,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.padchest.datamodule import make_split
+ from mednet.config.data.padchest.datamodule import make_split
database_checkers.check_split(
make_split(split),
@@ -56,7 +56,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.padchest"
+ f".{name}", "mednet.config.data.padchest"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_shenzhen.py b/tests/test_shenzhen.py
index b45ce0db..6658831b 100644
--- a/tests/test_shenzhen.py
+++ b/tests/test_shenzhen.py
@@ -34,7 +34,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.shenzhen.datamodule import make_split
+ from mednet.config.data.shenzhen.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -71,7 +71,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_summary.py b/tests/test_summary.py
index 0f3a7689..09b5398a 100644
--- a/tests/test_summary.py
+++ b/tests/test_summary.py
@@ -4,9 +4,9 @@
import unittest
-import ptbench.config.models.pasa as pasa_config
+import mednet.config.models.pasa as pasa_config
-from ptbench.utils.summary import summary
+from mednet.utils.summary import summary
class Tester(unittest.TestCase):
diff --git a/tests/test_tbpoc.py b/tests/test_tbpoc.py
index cf3327d4..a2704fa7 100644
--- a/tests/test_tbpoc.py
+++ b/tests/test_tbpoc.py
@@ -33,7 +33,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.tbpoc.datamodule import make_split
+ from mednet.config.data.tbpoc.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -72,7 +72,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.tbpoc"
+ f".{name}", "mednet.config.data.tbpoc"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_tbx11k.py b/tests/test_tbx11k.py
index 1b3a7222..39f0893d 100644
--- a/tests/test_tbx11k.py
+++ b/tests/test_tbx11k.py
@@ -138,7 +138,7 @@ def test_protocol_consistency(
lenghts: dict[str, int],
prefixes: typing.Sequence[str],
):
- from ptbench.config.data.tbx11k.datamodule import make_split
+ from mednet.config.data.tbx11k.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -251,7 +251,7 @@ def check_loaded_batch(
)
def test_loading(name: str, dataset: str, prefixes: typing.Sequence[str]):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.tbx11k"
+ f".{name}", "mednet.config.data.tbx11k"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_tranforms.py b/tests/test_tranforms.py
index 2c324aa1..651c4123 100644
--- a/tests/test_tranforms.py
+++ b/tests/test_tranforms.py
@@ -7,7 +7,7 @@ import numpy
import PIL.Image
import torchvision.transforms.functional as F
-from ptbench.data.augmentations import ElasticDeformation
+from mednet.data.augmentations import ElasticDeformation
def test_elastic_deformation(datadir):
--
GitLab