From b550794f771760e1b1903e2286c1d23b96ff345e Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Sun, 6 Aug 2023 15:55:04 +0200
Subject: [PATCH] Re-shuffle datamodules to the "config" base directory, adjust
tests and documentation
---
.reuse/dep5 | 4 +-
doc/_templates/config.rst | 5 +-
doc/api.rst | 38 ---
doc/config.rst | 125 ++++----
doc/links.rst | 4 +-
doc/results/index.rst | 30 +-
doc/usage/evaluation.rst | 2 +-
pyproject.toml | 270 +++++++++---------
.../{data/hivtb => config}/__init__.py | 0
.../indian => config/data/hivtb}/__init__.py | 0
.../{ => config}/data/hivtb/datamodule.py | 20 +-
.../{ => 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
src/ptbench/{ => config}/data/hivtb/fold_0.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_1.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_2.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_3.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_4.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_5.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_6.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_7.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_8.py | 4 +-
src/ptbench/{ => config}/data/hivtb/fold_9.py | 4 +-
.../data/indian}/__init__.py | 0
.../{ => config}/data/indian/datamodule.py | 16 +-
.../{ => 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 +-
.../data/montgomery}/__init__.py | 0
.../data/montgomery/datamodule.py | 20 +-
.../{ => config}/data/montgomery/default.json | 0
.../{ => config}/data/montgomery/default.py | 5 +-
.../{ => 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 | 5 +-
.../{ => config}/data/montgomery/fold_1.py | 5 +-
.../{ => config}/data/montgomery/fold_2.py | 5 +-
.../{ => config}/data/montgomery/fold_3.py | 5 +-
.../{ => config}/data/montgomery/fold_4.py | 5 +-
.../{ => config}/data/montgomery/fold_5.py | 5 +-
.../{ => config}/data/montgomery/fold_6.py | 5 +-
.../{ => config}/data/montgomery/fold_7.py | 5 +-
.../{ => config}/data/montgomery/fold_8.py | 5 +-
.../{ => config}/data/montgomery/fold_9.py | 5 +-
.../data/montgomery_shenzhen}/__init__.py | 0
.../data/montgomery_shenzhen/datamodule.py | 3 +-
.../data/montgomery_shenzhen/default.py | 0
.../data/montgomery_shenzhen/fold_0.py | 0
.../data/montgomery_shenzhen/fold_1.py | 0
.../data/montgomery_shenzhen/fold_2.py | 0
.../data/montgomery_shenzhen/fold_3.py | 0
.../data/montgomery_shenzhen/fold_4.py | 0
.../data/montgomery_shenzhen/fold_5.py | 0
.../data/montgomery_shenzhen/fold_6.py | 0
.../data/montgomery_shenzhen/fold_7.py | 0
.../data/montgomery_shenzhen/fold_8.py | 0
.../data/montgomery_shenzhen/fold_9.py | 0
.../montgomery_shenzhen_indian}/__init__.py | 0
.../montgomery_shenzhen_indian/datamodule.py | 24 +-
.../montgomery_shenzhen_indian/default.py | 0
.../data/montgomery_shenzhen_indian/fold_0.py | 0
.../data/montgomery_shenzhen_indian/fold_1.py | 0
.../data/montgomery_shenzhen_indian/fold_2.py | 0
.../data/montgomery_shenzhen_indian/fold_3.py | 0
.../data/montgomery_shenzhen_indian/fold_4.py | 0
.../data/montgomery_shenzhen_indian/fold_5.py | 0
.../data/montgomery_shenzhen_indian/fold_6.py | 0
.../data/montgomery_shenzhen_indian/fold_7.py | 0
.../data/montgomery_shenzhen_indian/fold_8.py | 0
.../data/montgomery_shenzhen_indian/fold_9.py | 0
.../__init__.py | 0
.../datamodule.py | 32 ++-
.../default.py | 0
.../__init__.py | 0
.../datamodule.py | 30 +-
.../v1_fold_0.py | 0
.../v1_fold_1.py | 0
.../v1_fold_2.py | 0
.../v1_fold_3.py | 0
.../v1_fold_4.py | 0
.../v1_fold_5.py | 0
.../v1_fold_6.py | 0
.../v1_fold_7.py | 0
.../v1_fold_8.py | 0
.../v1_fold_9.py | 0
.../v1_healthy_vs_atb.py | 0
.../v2_fold_0.py | 0
.../v2_fold_1.py | 0
.../v2_fold_2.py | 0
.../v2_fold_3.py | 0
.../v2_fold_4.py | 0
.../v2_fold_5.py | 0
.../v2_fold_6.py | 0
.../v2_fold_7.py | 0
.../v2_fold_8.py | 0
.../v2_fold_9.py | 0
.../v2_others_vs_atb.py | 0
.../data/nih_cxr14}/__init__.py | 0
.../data/nih_cxr14/cardiomegaly.json | 0
.../data/nih_cxr14/cardiomegaly.py | 5 +-
.../{ => config}/data/nih_cxr14/datamodule.py | 33 ++-
.../data/nih_cxr14/default.json.bz2 | Bin
.../{ => config}/data/nih_cxr14/default.py | 5 +-
.../data/nih_cxr14_padchest}/__init__.py | 0
.../data/nih_cxr14_padchest/datamodule.py | 18 +-
.../data/nih_cxr14_padchest/idiap.py | 0
.../data/padchest}/__init__.py | 0
.../data/padchest/cardiomegaly-idiap.json | 0
.../data/padchest/cardiomegaly_idiap.py | 6 +-
.../{ => config}/data/padchest/datamodule.py | 22 +-
.../{ => config}/data/padchest/idiap.json.bz2 | Bin
.../{ => config}/data/padchest/idiap.py | 9 +-
.../data/padchest/no-tb-idiap.json.bz2 | Bin
.../{ => config}/data/padchest/no_tb_idiap.py | 5 +-
.../{ => config}/data/padchest/tb-idiap.json | 0
.../{ => config}/data/padchest/tb_idiap.py | 5 +-
.../data/shenzhen}/__init__.py | 0
.../{ => config}/data/shenzhen/datamodule.py | 22 +-
.../{ => config}/data/shenzhen/default.json | 0
.../{ => config}/data/shenzhen/default.py | 5 +-
.../{ => 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 | 5 +-
.../{ => config}/data/shenzhen/fold_1.py | 5 +-
.../{ => config}/data/shenzhen/fold_2.py | 5 +-
.../{ => config}/data/shenzhen/fold_3.py | 5 +-
.../{ => config}/data/shenzhen/fold_4.py | 5 +-
.../{ => config}/data/shenzhen/fold_5.py | 5 +-
.../{ => config}/data/shenzhen/fold_6.py | 5 +-
.../{ => config}/data/shenzhen/fold_7.py | 5 +-
.../{ => config}/data/shenzhen/fold_8.py | 5 +-
.../{ => config}/data/shenzhen/fold_9.py | 5 +-
.../tbx11k => config/data/tbpoc}/__init__.py | 0
.../{ => config}/data/tbpoc/datamodule.py | 22 +-
.../{ => 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
src/ptbench/{ => config}/data/tbpoc/fold_0.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_1.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_2.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_3.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_4.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_5.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_6.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_7.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_8.py | 5 +-
src/ptbench/{ => config}/data/tbpoc/fold_9.py | 5 +-
.../config => config/data/tbx11k}/__init__.py | 0
.../{ => config}/data/tbx11k/datamodule.py | 19 +-
.../data/tbx11k/make_splits_from_database.py | 0
.../{ => 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
.../data/tbx11k/v1-healthy-vs-atb.json | 0
.../{ => config}/data/tbx11k/v1_fold_0.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_1.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_2.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_3.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_4.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_5.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_6.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_7.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_8.py | 5 +-
.../{ => config}/data/tbx11k/v1_fold_9.py | 5 +-
.../data/tbx11k/v1_healthy_vs_atb.py | 5 +-
.../{ => 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
.../data/tbx11k/v2-others-vs-atb.json | 0
.../{ => config}/data/tbx11k/v2_fold_0.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_1.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_2.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_3.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_4.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_5.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_6.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_7.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_8.py | 5 +-
.../{ => config}/data/tbx11k/v2_fold_9.py | 5 +-
.../data/tbx11k/v2_others_vs_atb.py | 5 +-
src/ptbench/config/models/__init__.py | 0
.../config => config/models}/alexnet.py | 2 +-
.../models}/alexnet_pretrained.py | 0
.../config => config/models}/densenet.py | 0
.../models}/densenet_pretrained.py | 0
.../config => config/models}/densenet_rs.py | 0
.../models}/logistic_regression.py | 0
.../{models/config => config/models}/mlp.py | 0
.../{models/config => config/models}/pasa.py | 0
tests/test_cli.py | 8 +-
tests/test_hivtb.py | 4 +-
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 | 19 +-
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 | 2 +-
tests/test_tbpoc.py | 4 +-
tests/test_tbx11k.py | 4 +-
268 files changed, 703 insertions(+), 560 deletions(-)
rename src/ptbench/{data/hivtb => config}/__init__.py (100%)
rename src/ptbench/{data/indian => config/data/hivtb}/__init__.py (100%)
rename src/ptbench/{ => config}/data/hivtb/datamodule.py (85%)
rename src/ptbench/{ => config}/data/hivtb/fold-0.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-1.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-2.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-3.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-4.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-5.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-6.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-7.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-8.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold-9.json (100%)
rename src/ptbench/{ => config}/data/hivtb/fold_0.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_1.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_2.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_3.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_4.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_5.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_6.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_7.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_8.py (65%)
rename src/ptbench/{ => config}/data/hivtb/fold_9.py (65%)
rename src/ptbench/{data/montgomery => config/data/indian}/__init__.py (100%)
rename src/ptbench/{ => config}/data/indian/datamodule.py (78%)
rename src/ptbench/{ => config}/data/indian/default.json (100%)
rename src/ptbench/{ => config}/data/indian/default.py (65%)
rename src/ptbench/{ => config}/data/indian/fold-0.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-1.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-2.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-3.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-4.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-5.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-6.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-7.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-8.json (100%)
rename src/ptbench/{ => config}/data/indian/fold-9.json (100%)
rename src/ptbench/{ => config}/data/indian/fold_0.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_1.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_2.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_3.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_4.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_5.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_6.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_7.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_8.py (66%)
rename src/ptbench/{ => config}/data/indian/fold_9.py (66%)
rename src/ptbench/{data/montgomery_shenzhen => config/data/montgomery}/__init__.py (100%)
rename src/ptbench/{ => config}/data/montgomery/datamodule.py (86%)
rename src/ptbench/{ => config}/data/montgomery/default.json (100%)
rename src/ptbench/{ => config}/data/montgomery/default.py (63%)
rename src/ptbench/{ => config}/data/montgomery/fold-0.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-1.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-2.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-3.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-4.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-5.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-6.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-7.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-8.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold-9.json (100%)
rename src/ptbench/{ => config}/data/montgomery/fold_0.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_1.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_2.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_3.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_4.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_5.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_6.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_7.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_8.py (65%)
rename src/ptbench/{ => config}/data/montgomery/fold_9.py (65%)
rename src/ptbench/{data/montgomery_shenzhen_indian => config/data/montgomery_shenzhen}/__init__.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/datamodule.py (96%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/default.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_0.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_1.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_2.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_3.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_4.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_5.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_6.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_7.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_8.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen/fold_9.py (100%)
rename src/ptbench/{data/montgomery_shenzhen_indian_padchest => config/data/montgomery_shenzhen_indian}/__init__.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/datamodule.py (70%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/default.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_0.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_1.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_2.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_3.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_4.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_5.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_6.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_7.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_8.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian/fold_9.py (100%)
rename src/ptbench/{data/montgomery_shenzhen_indian_tbx11k => config/data/montgomery_shenzhen_indian_padchest}/__init__.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_padchest/datamodule.py (70%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_padchest/default.py (100%)
rename src/ptbench/{data/nih_cxr14 => config/data/montgomery_shenzhen_indian_tbx11k}/__init__.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/datamodule.py (69%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py (100%)
rename src/ptbench/{ => config}/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py (100%)
rename src/ptbench/{data/nih_cxr14_padchest => config/data/nih_cxr14}/__init__.py (100%)
rename src/ptbench/{ => config}/data/nih_cxr14/cardiomegaly.json (100%)
rename src/ptbench/{ => config}/data/nih_cxr14/cardiomegaly.py (71%)
rename src/ptbench/{ => config}/data/nih_cxr14/datamodule.py (82%)
rename src/ptbench/{ => config}/data/nih_cxr14/default.json.bz2 (100%)
rename src/ptbench/{ => config}/data/nih_cxr14/default.py (67%)
rename src/ptbench/{data/padchest => config/data/nih_cxr14_padchest}/__init__.py (100%)
rename src/ptbench/{ => config}/data/nih_cxr14_padchest/datamodule.py (73%)
rename src/ptbench/{ => config}/data/nih_cxr14_padchest/idiap.py (100%)
rename src/ptbench/{data/shenzhen => config/data/padchest}/__init__.py (100%)
rename src/ptbench/{ => config}/data/padchest/cardiomegaly-idiap.json (100%)
rename src/ptbench/{ => config}/data/padchest/cardiomegaly_idiap.py (72%)
rename src/ptbench/{ => config}/data/padchest/datamodule.py (94%)
rename src/ptbench/{ => config}/data/padchest/idiap.json.bz2 (100%)
rename src/ptbench/{ => config}/data/padchest/idiap.py (67%)
rename src/ptbench/{ => config}/data/padchest/no-tb-idiap.json.bz2 (100%)
rename src/ptbench/{ => config}/data/padchest/no_tb_idiap.py (81%)
rename src/ptbench/{ => config}/data/padchest/tb-idiap.json (100%)
rename src/ptbench/{ => config}/data/padchest/tb_idiap.py (77%)
rename src/ptbench/{data/tbpoc => config/data/shenzhen}/__init__.py (100%)
rename src/ptbench/{ => config}/data/shenzhen/datamodule.py (84%)
rename src/ptbench/{ => config}/data/shenzhen/default.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/default.py (75%)
rename src/ptbench/{ => config}/data/shenzhen/fold-0.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-1.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-2.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-3.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-4.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-5.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-6.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-7.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-8.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold-9.json (100%)
rename src/ptbench/{ => config}/data/shenzhen/fold_0.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_1.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_2.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_3.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_4.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_5.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_6.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_7.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_8.py (66%)
rename src/ptbench/{ => config}/data/shenzhen/fold_9.py (66%)
rename src/ptbench/{data/tbx11k => config/data/tbpoc}/__init__.py (100%)
rename src/ptbench/{ => config}/data/tbpoc/datamodule.py (84%)
rename src/ptbench/{ => config}/data/tbpoc/fold-0.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-1.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-2.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-3.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-4.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-5.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-6.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-7.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-8.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold-9.json (100%)
rename src/ptbench/{ => config}/data/tbpoc/fold_0.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_1.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_2.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_3.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_4.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_5.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_6.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_7.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_8.py (65%)
rename src/ptbench/{ => config}/data/tbpoc/fold_9.py (65%)
rename src/ptbench/{models/config => config/data/tbx11k}/__init__.py (100%)
rename src/ptbench/{ => config}/data/tbx11k/datamodule.py (93%)
rename src/ptbench/{ => config}/data/tbx11k/make_splits_from_database.py (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-0.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-1.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-2.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-3.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-4.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-5.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-6.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-7.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-8.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-fold-9.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1-healthy-vs-atb.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_0.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_1.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_2.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_3.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_4.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_5.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_6.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_7.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_8.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_fold_9.py (67%)
rename src/ptbench/{ => config}/data/tbx11k/v1_healthy_vs_atb.py (81%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-0.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-1.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-2.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-3.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-4.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-5.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-6.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-7.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-8.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-fold-9.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2-others-vs-atb.json (100%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_0.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_1.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_2.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_3.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_4.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_5.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_6.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_7.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_8.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_fold_9.py (68%)
rename src/ptbench/{ => config}/data/tbx11k/v2_others_vs_atb.py (83%)
create mode 100644 src/ptbench/config/models/__init__.py
rename src/ptbench/{models/config => config/models}/alexnet.py (90%)
rename src/ptbench/{models/config => config/models}/alexnet_pretrained.py (100%)
rename src/ptbench/{models/config => config/models}/densenet.py (100%)
rename src/ptbench/{models/config => config/models}/densenet_pretrained.py (100%)
rename src/ptbench/{models/config => config/models}/densenet_rs.py (100%)
rename src/ptbench/{models/config => config/models}/logistic_regression.py (100%)
rename src/ptbench/{models/config => config/models}/mlp.py (100%)
rename src/ptbench/{models/config => config/models}/pasa.py (100%)
diff --git a/.reuse/dep5 b/.reuse/dep5
index f21f6e2e..4e2a69c2 100644
--- a/.reuse/dep5
+++ b/.reuse/dep5
@@ -15,8 +15,8 @@ Files:
doc/results/img/*.jpg
doc/results/img/*.png
doc/results/img/*/*.jpg
- src/ptbench/data/*/*.json
- src/ptbench/data/*/*.json.bz2
+ src/ptbench/config/data/*/*.json
+ src/ptbench/config/data/*/*.json.bz2
tests/data/*.csv
tests/data/*.json
tests/data/*.png
diff --git a/doc/_templates/config.rst b/doc/_templates/config.rst
index 3a1f3d38..dc8a8877 100644
--- a/doc/_templates/config.rst
+++ b/doc/_templates/config.rst
@@ -1,3 +1,6 @@
{% include "autosummary/module.rst" %}
-.. literalinclude:: ../../../../src/{{ fullname.replace(".", "/") }}.py
+.. literalinclude:: ../../../src/{{ fullname.replace(".", "/") }}.py
:start-at: import
+
+
+.. include:: ../../links.rst
diff --git a/doc/api.rst b/doc/api.rst
index 5bfd2b2f..4b223ca5 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -28,44 +28,6 @@ Auxiliary classes and methods to define raw dataset iterators.
ptbench.data.split
ptbench.data.typing
-.. _ptbench.api.rawdata:
-
-Basic Datamodules
------------------
-
-Pytorch_ :py:class:`torch.utils.data.DataLoader` access through lightning_
-:py:class:`lightning.pytorch.core.LightningDataModule`.
-
-.. autosummary::
- :toctree: api/data/raw
-
- ptbench.data.hivtb.datamodule
- ptbench.data.indian.datamodule
- ptbench.data.montgomery.datamodule
- ptbench.data.nih_cxr14.datamodule
- ptbench.data.padchest.datamodule
- ptbench.data.shenzhen.datamodule
- ptbench.data.tbpoc.datamodule
- ptbench.data.tbx11k.datamodule
-
-
-.. _ptbench.api.remixdata:
-
-Remixed Datamodules
--------------------
-
-Pytorch_ :py:class:`torch.utils.data.DataLoader` access through lightning_
-:py:class:`lightning.pytorch.core.LightningDataModule`.
-
-.. autosummary::
- :toctree: api/data/raw
-
- ptbench.data.montgomery_shenzhen.datamodule
- ptbench.data.montgomery_shenzhen_indian.datamodule
- ptbench.data.montgomery_shenzhen_indian_tbx11k.datamodule
- ptbench.data.montgomery_shenzhen_indian_padchest.datamodule
- ptbench.data.nih_cxr14_padchest.datamodule
-
.. _ptbench.api.models:
diff --git a/doc/config.rst b/doc/config.rst
index cedc8c07..93c4559a 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -13,68 +13,86 @@ datamodules.
.. _ptbench.config.models:
-Models
-======
+Pre-configured Models
+=====================
+
+Pre-configured models you can readily use.
.. autosummary::
- :toctree: api/models/config
+ :toctree: api/config.models
:template: config.rst
- ptbench.models.config.alexnet
- ptbench.models.config.alexnet_pretrained
- ptbench.models.config.densenet
- ptbench.models.config.densenet_pretrained
- ptbench.models.config.densenet_rs
- ptbench.models.config.logistic_regression
- ptbench.models.config.mlp
- ptbench.models.config.pasa
+ 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
.. _ptbench.config.datamodules:
-Preset Datamodules
+DataModule support
==================
-Datamodules include iterative accessors to raw data
-(:ref:`ptbench.setup.databases`) including data pre-processing to a minimum
-input standard, if applicable. Use these datamodules for training and evaluating
-your models.
+Base DataModules and raw data loaders for the various databases currently
+supported in this package, for your reference. Each pre-configured data module
+can receive the name of one or more splits as argument to build a fully
+functional data module that can be used in training, prediction or testing.
.. autosummary::
- :toctree: api/data/config
- :template: config.rst
+ :toctree: api/config.datamodules
- ptbench.data.indian.default
- ptbench.data.montgomery.default
- ptbench.data.nih_cxr14.default
- ptbench.data.padchest.idiap
- ptbench.data.shenzhen.default
- ptbench.data.tbx11k.v1_healthy_vs_atb
- ptbench.data.tbx11k.v2_others_vs_atb
+ 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
-.. _ptbench.config.datamodules.remix:
+.. _ptbench.config.datamodule-instances:
-Remix Datamodules
-=================
+Pre-configured DataModules
+==========================
-We provide some aggregated datamodules to facilitate cross-database development.
+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>`.
.. autosummary::
- :toctree: api/data/config
+ :toctree: api/config.datamodule-instances
:template: config.rst
- ptbench.data.montgomery_shenzhen.default
- ptbench.data.montgomery_shenzhen_indian.default
- ptbench.data.montgomery_shenzhen_indian_padchest.default
- ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
- ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
- ptbench.data.nih_cxr14_padchest.idiap
-
-
-.. _ptbench.config.datamodules.folds:
-
-Cross-validation Datamodules
+ 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
+
+
+.. _ptbench.config.datamodule-instances.folds:
+
+Cross-validation DataModules
============================
We support cross-validation with precise preset folds. In this section, you
@@ -84,19 +102,20 @@ datamodules. Nine other folds are available for every configuration (from 1 to
.. autosummary::
- :toctree: api/data/config
+ :toctree: api/config.datamodule-folds
:template: config.rst
- ptbench.data.hivtb.fold_0
- ptbench.data.indian.fold_0
- ptbench.data.montgomery.fold_0
- ptbench.data.montgomery_shenzhen.fold_0
- ptbench.data.montgomery_shenzhen_indian.fold_0
- ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
- ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
- ptbench.data.shenzhen.fold_0
- ptbench.data.tbpoc.fold_0
- ptbench.data.tbx11k.v1_fold_0
- ptbench.data.tbx11k.v2_fold_0
+ 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
+
.. include:: links.rst
diff --git a/doc/links.rst b/doc/links.rst
index 2e454082..f4ba3310 100644
--- a/doc/links.rst
+++ b/doc/links.rst
@@ -25,6 +25,6 @@
.. models
.. _imagenet: https://www.image-net.org
.. _alexnet: https://en.wikipedia.org/wiki/AlexNet
-.. _alexnet_pytorch: https://pytorch.org/hub/pytorch_vision_alexnet/
+.. _alexnet-pytorch: https://pytorch.org/hub/pytorch_vision_alexnet/
.. _densenet: https://arxiv.org/abs/1608.06993
-.. _densenet_pytorch: https://pytorch.org/hub/pytorch_vision_densenet/
+.. _densenet-pytorch: https://pytorch.org/hub/pytorch_vision_densenet/
diff --git a/doc/results/index.rst b/doc/results/index.rst
index 0217fe6c..0585e912 100644
--- a/doc/results/index.rst
+++ b/doc/results/index.rst
@@ -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.models.config.pasa>`: Pasa trained on normalized-kfold MC
+ :py:mod:`Pasa <ptbench.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.models.config.pasa>`: Pasa trained on normalized-kfold MC-CH
+ :py:mod:`Pasa <ptbench.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.models.config.pasa>`: Pasa trained on normalized-kfold MC-CH-IN
+ :py:mod:`Pasa <ptbench.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.models.config.densenet>`: DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>`: DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>` DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>` DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>` DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <ptbench.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.models.config.logistic_regression>`: LogReg trained on normalized-kfold MC
+ :py:mod:`LogReg <ptbench.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.models.config.logistic_regression>`: LogReg trained on normalized-kfold MC-CH
+ :py:mod:`LogReg <ptbench.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.models.config.logistic_regression>`: LogReg trained on normalized-kfold MC-CH-IN
+ :py:mod:`LogReg <ptbench.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.models.config.densenet>`: DenseNet trained on normalized-kfold MC (pretrained on NIH)
+ :py:mod:`DenseNet <ptbench.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.models.config.densenet>`: DenseNet 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)
- .. 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.models.config.densenet>`: DenseNet 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)
Global sensitivity analysis (relevance)
diff --git a/doc/usage/evaluation.rst b/doc/usage/evaluation.rst
index 8d98ca92..1778e126 100644
--- a/doc/usage/evaluation.rst
+++ b/doc/usage/evaluation.rst
@@ -35,7 +35,7 @@ the pre-trained model.
.. tip::
An option to generate grad-CAMs is available for the :py:mod:`DensenetRS
- <ptbench.models.config.densenet_rs>` model. To activate it, use the
+ <ptbench.config.models.densenet_rs>` model. To activate it, use the
``--grad-cams`` argument.
.. tip::
diff --git a/pyproject.toml b/pyproject.toml
index f2de6fd4..8ebe16e4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ dependencies = [
"torch>=1.8",
"torchvision>=0.10",
"lightning>=2.0.3",
- "pydantic <2.0,>=1.7.4", # temporary, until issue #31 is fixed
+ "pydantic <2.0,>=1.7.4", # temporary, until issue #31 is fixed
"tensorboard",
]
@@ -70,168 +70,168 @@ ptbench = "ptbench.scripts.cli:cli"
[project.entry-points."ptbench.config"]
# models
-pasa = "ptbench.models.config.pasa"
-mlp = "ptbench.models.config.mlp"
-logistic-regression = "ptbench.models.config.logistic_regression"
-alexnet = "ptbench.models.config.alexnet"
-alexnet-pretrained = "ptbench.models.config.alexnet_pretrained"
-densenet = "ptbench.models.config.densenet"
-densenet-pretrained = "ptbench.models.config.densenet_pretrained"
+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"
# montgomery dataset (and cross-validation folds)
-montgomery = "ptbench.data.montgomery.default"
-montgomery-f0 = "ptbench.data.montgomery.fold_0"
-montgomery-f1 = "ptbench.data.montgomery.fold_1"
-montgomery-f2 = "ptbench.data.montgomery.fold_2"
-montgomery-f3 = "ptbench.data.montgomery.fold_3"
-montgomery-f4 = "ptbench.data.montgomery.fold_4"
-montgomery-f5 = "ptbench.data.montgomery.fold_5"
-montgomery-f6 = "ptbench.data.montgomery.fold_6"
-montgomery-f7 = "ptbench.data.montgomery.fold_7"
-montgomery-f8 = "ptbench.data.montgomery.fold_8"
-montgomery-f9 = "ptbench.data.montgomery.fold_9"
+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"
# shenzhen dataset (and cross-validation folds)
-shenzhen = "ptbench.data.shenzhen.default"
-shenzhen-f0 = "ptbench.data.shenzhen.fold_0"
-shenzhen-f1 = "ptbench.data.shenzhen.fold_1"
-shenzhen-f2 = "ptbench.data.shenzhen.fold_2"
-shenzhen-f3 = "ptbench.data.shenzhen.fold_3"
-shenzhen-f4 = "ptbench.data.shenzhen.fold_4"
-shenzhen-f5 = "ptbench.data.shenzhen.fold_5"
-shenzhen-f6 = "ptbench.data.shenzhen.fold_6"
-shenzhen-f7 = "ptbench.data.shenzhen.fold_7"
-shenzhen-f8 = "ptbench.data.shenzhen.fold_8"
-shenzhen-f9 = "ptbench.data.shenzhen.fold_9"
+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"
# indian dataset (and cross-validation folds)
-indian = "ptbench.data.indian.default"
-indian-f0 = "ptbench.data.indian.fold_0"
-indian-f1 = "ptbench.data.indian.fold_1"
-indian-f2 = "ptbench.data.indian.fold_2"
-indian-f3 = "ptbench.data.indian.fold_3"
-indian-f4 = "ptbench.data.indian.fold_4"
-indian-f5 = "ptbench.data.indian.fold_5"
-indian-f6 = "ptbench.data.indian.fold_6"
-indian-f7 = "ptbench.data.indian.fold_7"
-indian-f8 = "ptbench.data.indian.fold_8"
-indian-f9 = "ptbench.data.indian.fold_9"
+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"
# TBX11K dataset split 1: healthy vs active tb, and cross-validation folds
-tbx11k-v1-healthy-vs-atb = "ptbench.data.tbx11k.v1_healthy_vs_atb"
-tbx11k-v1-f0 = "ptbench.data.tbx11k.v1_fold_0"
-tbx11k-v1-f1 = "ptbench.data.tbx11k.v1_fold_1"
-tbx11k-v1-f2 = "ptbench.data.tbx11k.v1_fold_2"
-tbx11k-v1-f3 = "ptbench.data.tbx11k.v1_fold_3"
-tbx11k-v1-f4 = "ptbench.data.tbx11k.v1_fold_4"
-tbx11k-v1-f5 = "ptbench.data.tbx11k.v1_fold_5"
-tbx11k-v1-f6 = "ptbench.data.tbx11k.v1_fold_6"
-tbx11k-v1-f7 = "ptbench.data.tbx11k.v1_fold_7"
-tbx11k-v1-f8 = "ptbench.data.tbx11k.v1_fold_8"
-tbx11k-v1-f9 = "ptbench.data.tbx11k.v1_fold_9"
+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 dataset split 2: others vs active tb, and cross-validation folds
-tbx11k-v2-others-vs-atb = "ptbench.data.tbx11k.v2_others_vs_atb"
-tbx11k-v2-f0 = "ptbench.data.tbx11k.v2_fold_0"
-tbx11k-v2-f1 = "ptbench.data.tbx11k.v2_fold_1"
-tbx11k-v2-f2 = "ptbench.data.tbx11k.v2_fold_2"
-tbx11k-v2-f3 = "ptbench.data.tbx11k.v2_fold_3"
-tbx11k-v2-f4 = "ptbench.data.tbx11k.v2_fold_4"
-tbx11k-v2-f5 = "ptbench.data.tbx11k.v2_fold_5"
-tbx11k-v2-f6 = "ptbench.data.tbx11k.v2_fold_6"
-tbx11k-v2-f7 = "ptbench.data.tbx11k.v2_fold_7"
-tbx11k-v2-f8 = "ptbench.data.tbx11k.v2_fold_8"
-tbx11k-v2-f9 = "ptbench.data.tbx11k.v2_fold_9"
+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"
# montgomery-shenzhen aggregated dataset
-montgomery-shenzhen = "ptbench.data.montgomery_shenzhen.default"
-montgomery-shenzhen-f0 = "ptbench.data.montgomery_shenzhen.fold_0"
-montgomery-shenzhen-f1 = "ptbench.data.montgomery_shenzhen.fold_1"
-montgomery-shenzhen-f2 = "ptbench.data.montgomery_shenzhen.fold_2"
-montgomery-shenzhen-f3 = "ptbench.data.montgomery_shenzhen.fold_3"
-montgomery-shenzhen-f4 = "ptbench.data.montgomery_shenzhen.fold_4"
-montgomery-shenzhen-f5 = "ptbench.data.montgomery_shenzhen.fold_5"
-montgomery-shenzhen-f6 = "ptbench.data.montgomery_shenzhen.fold_6"
-montgomery-shenzhen-f7 = "ptbench.data.montgomery_shenzhen.fold_7"
-montgomery-shenzhen-f8 = "ptbench.data.montgomery_shenzhen.fold_8"
-montgomery-shenzhen-f9 = "ptbench.data.montgomery_shenzhen.fold_9"
+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-indian aggregated dataset
-montgomery-shenzhen-indian = "ptbench.data.montgomery_shenzhen_indian.default"
-montgomery-shenzhen-indian-f0 = "ptbench.data.montgomery_shenzhen_indian.fold_0"
-montgomery-shenzhen-indian-f1 = "ptbench.data.montgomery_shenzhen_indian.fold_1"
-montgomery-shenzhen-indian-f2 = "ptbench.data.montgomery_shenzhen_indian.fold_2"
-montgomery-shenzhen-indian-f3 = "ptbench.data.montgomery_shenzhen_indian.fold_3"
-montgomery-shenzhen-indian-f4 = "ptbench.data.montgomery_shenzhen_indian.fold_4"
-montgomery-shenzhen-indian-f5 = "ptbench.data.montgomery_shenzhen_indian.fold_5"
-montgomery-shenzhen-indian-f6 = "ptbench.data.montgomery_shenzhen_indian.fold_6"
-montgomery-shenzhen-indian-f7 = "ptbench.data.montgomery_shenzhen_indian.fold_7"
-montgomery-shenzhen-indian-f8 = "ptbench.data.montgomery_shenzhen_indian.fold_8"
-montgomery-shenzhen-indian-f9 = "ptbench.data.montgomery_shenzhen_indian.fold_9"
+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-tbx11k aggregated dataset
-montgomery-shenzhen-indian-tbx11k-v1 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v1-f0 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0"
-montgomery-shenzhen-indian-tbx11k-v1-f1 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1"
-montgomery-shenzhen-indian-tbx11k-v1-f2 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2"
-montgomery-shenzhen-indian-tbx11k-v1-f3 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3"
-montgomery-shenzhen-indian-tbx11k-v1-f4 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4"
-montgomery-shenzhen-indian-tbx11k-v1-f5 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5"
-montgomery-shenzhen-indian-tbx11k-v1-f6 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6"
-montgomery-shenzhen-indian-tbx11k-v1-f7 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7"
-montgomery-shenzhen-indian-tbx11k-v1-f8 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8"
-montgomery-shenzhen-indian-tbx11k-v1-f9 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9"
-montgomery-shenzhen-indian-tbx11k-v2 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v2-f0 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0"
-montgomery-shenzhen-indian-tbx11k-v2-f1 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1"
-montgomery-shenzhen-indian-tbx11k-v2-f2 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2"
-montgomery-shenzhen-indian-tbx11k-v2-f3 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3"
-montgomery-shenzhen-indian-tbx11k-v2-f4 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4"
-montgomery-shenzhen-indian-tbx11k-v2-f5 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5"
-montgomery-shenzhen-indian-tbx11k-v2-f6 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6"
-montgomery-shenzhen-indian-tbx11k-v2-f7 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7"
-montgomery-shenzhen-indian-tbx11k-v2-f8 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8"
-montgomery-shenzhen-indian-tbx11k-v2-f9 = "ptbench.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9"
+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"
# tbpoc dataset (only cross-validation folds)
-tbpoc-f0 = "ptbench.data.tbpoc.fold_0"
-tbpoc-f1 = "ptbench.data.tbpoc.fold_1"
-tbpoc-f2 = "ptbench.data.tbpoc.fold_2"
-tbpoc-f3 = "ptbench.data.tbpoc.fold_3"
-tbpoc-f4 = "ptbench.data.tbpoc.fold_4"
-tbpoc-f5 = "ptbench.data.tbpoc.fold_5"
-tbpoc-f6 = "ptbench.data.tbpoc.fold_6"
-tbpoc-f7 = "ptbench.data.tbpoc.fold_7"
-tbpoc-f8 = "ptbench.data.tbpoc.fold_8"
-tbpoc-f9 = "ptbench.data.tbpoc.fold_9"
+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"
# hivtb dataset (only cross-validation folds)
-hivtb-f0 = "ptbench.data.hivtb.fold_0"
-hivtb-f1 = "ptbench.data.hivtb.fold_1"
-hivtb-f2 = "ptbench.data.hivtb.fold_2"
-hivtb-f3 = "ptbench.data.hivtb.fold_3"
-hivtb-f4 = "ptbench.data.hivtb.fold_4"
-hivtb-f5 = "ptbench.data.hivtb.fold_5"
-hivtb-f6 = "ptbench.data.hivtb.fold_6"
-hivtb-f7 = "ptbench.data.hivtb.fold_7"
-hivtb-f8 = "ptbench.data.hivtb.fold_8"
-hivtb-f9 = "ptbench.data.hivtb.fold_9"
+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"
# NIH CXR14 (relabeled), multi-class (14 labels)
-nih-cxr14 = "ptbench.data.nih_cxr14.default"
-nih-cxr14-cardiomegaly = "ptbench.data.nih_cxr14.cardiomegaly"
+nih-cxr14 = "ptbench.config.data.nih_cxr14.default"
+nih-cxr14-cardiomegaly = "ptbench.config.data.nih_cxr14.cardiomegaly"
# PadChest, multi-class (varied number of labels)
-padchest-idiap = "ptbench.data.padchest.idiap"
-padchest-tb-idiap = "ptbench.data.padchest.tb_idiap"
-padchest-no-tb-idiap = "ptbench.data.padchest.no_tb_idiap"
-padchest-cardiomegaly-idiap = "ptbench.data.padchest.cardiomegaly_idiap"
+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"
# NIH CXR14 / PadChest aggregated dataset
-nih-cxr14-padchest = "ptbench.data.nih_cxr14_padchest.idiap"
+nih-cxr14-padchest = "ptbench.config.data.nih_cxr14_padchest.idiap"
# montgomery-shenzhen-indian-padchest aggregated dataset
-montgomery-shenzhen-indian-padchest = "ptbench.data.montgomery_shenzhen_indian_padchest.default"
+montgomery-shenzhen-indian-padchest = "ptbench.config.data.montgomery_shenzhen_indian_padchest.default"
[tool.setuptools]
zip-safe = true
diff --git a/src/ptbench/data/hivtb/__init__.py b/src/ptbench/config/__init__.py
similarity index 100%
rename from src/ptbench/data/hivtb/__init__.py
rename to src/ptbench/config/__init__.py
diff --git a/src/ptbench/data/indian/__init__.py b/src/ptbench/config/data/hivtb/__init__.py
similarity index 100%
rename from src/ptbench/data/indian/__init__.py
rename to src/ptbench/config/data/hivtb/__init__.py
diff --git a/src/ptbench/data/hivtb/datamodule.py b/src/ptbench/config/data/hivtb/datamodule.py
similarity index 85%
rename from src/ptbench/data/hivtb/datamodule.py
rename to src/ptbench/config/data/hivtb/datamodule.py
index 2c68c85d..653743a5 100644
--- a/src/ptbench/data/hivtb/datamodule.py
+++ b/src/ptbench/config/data/hivtb/datamodule.py
@@ -14,13 +14,17 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..image_utils import remove_black_borders
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
class RawDataLoader(_BaseRawDataLoader):
@@ -32,7 +36,7 @@ class RawDataLoader(_BaseRawDataLoader):
def __init__(self):
self.datadir = load_rc().get(
- "datadir.hivtb", os.path.realpath(os.curdir)
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
)
def sample(self, sample: tuple[str, int]) -> Sample:
diff --git a/src/ptbench/data/hivtb/fold-0.json b/src/ptbench/config/data/hivtb/fold-0.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-0.json
rename to src/ptbench/config/data/hivtb/fold-0.json
diff --git a/src/ptbench/data/hivtb/fold-1.json b/src/ptbench/config/data/hivtb/fold-1.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-1.json
rename to src/ptbench/config/data/hivtb/fold-1.json
diff --git a/src/ptbench/data/hivtb/fold-2.json b/src/ptbench/config/data/hivtb/fold-2.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-2.json
rename to src/ptbench/config/data/hivtb/fold-2.json
diff --git a/src/ptbench/data/hivtb/fold-3.json b/src/ptbench/config/data/hivtb/fold-3.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-3.json
rename to src/ptbench/config/data/hivtb/fold-3.json
diff --git a/src/ptbench/data/hivtb/fold-4.json b/src/ptbench/config/data/hivtb/fold-4.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-4.json
rename to src/ptbench/config/data/hivtb/fold-4.json
diff --git a/src/ptbench/data/hivtb/fold-5.json b/src/ptbench/config/data/hivtb/fold-5.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-5.json
rename to src/ptbench/config/data/hivtb/fold-5.json
diff --git a/src/ptbench/data/hivtb/fold-6.json b/src/ptbench/config/data/hivtb/fold-6.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-6.json
rename to src/ptbench/config/data/hivtb/fold-6.json
diff --git a/src/ptbench/data/hivtb/fold-7.json b/src/ptbench/config/data/hivtb/fold-7.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-7.json
rename to src/ptbench/config/data/hivtb/fold-7.json
diff --git a/src/ptbench/data/hivtb/fold-8.json b/src/ptbench/config/data/hivtb/fold-8.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-8.json
rename to src/ptbench/config/data/hivtb/fold-8.json
diff --git a/src/ptbench/data/hivtb/fold-9.json b/src/ptbench/config/data/hivtb/fold-9.json
similarity index 100%
rename from src/ptbench/data/hivtb/fold-9.json
rename to src/ptbench/config/data/hivtb/fold-9.json
diff --git a/src/ptbench/data/hivtb/fold_0.py b/src/ptbench/config/data/hivtb/fold_0.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_0.py
rename to src/ptbench/config/data/hivtb/fold_0.py
index c8a11de1..4e00590f 100644
--- a/src/ptbench/data/hivtb/fold_0.py
+++ b/src/ptbench/config/data/hivtb/fold_0.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/data/hivtb/fold_1.py b/src/ptbench/config/data/hivtb/fold_1.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_1.py
rename to src/ptbench/config/data/hivtb/fold_1.py
index 3b2434e0..55333dd0 100644
--- a/src/ptbench/data/hivtb/fold_1.py
+++ b/src/ptbench/config/data/hivtb/fold_1.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/data/hivtb/fold_2.py b/src/ptbench/config/data/hivtb/fold_2.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_2.py
rename to src/ptbench/config/data/hivtb/fold_2.py
index ac95eca1..5c8fd9b7 100644
--- a/src/ptbench/data/hivtb/fold_2.py
+++ b/src/ptbench/config/data/hivtb/fold_2.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/data/hivtb/fold_3.py b/src/ptbench/config/data/hivtb/fold_3.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_3.py
rename to src/ptbench/config/data/hivtb/fold_3.py
index 1d662e27..5d1b308c 100644
--- a/src/ptbench/data/hivtb/fold_3.py
+++ b/src/ptbench/config/data/hivtb/fold_3.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/data/hivtb/fold_4.py b/src/ptbench/config/data/hivtb/fold_4.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_4.py
rename to src/ptbench/config/data/hivtb/fold_4.py
index 1f59dcf5..77c2073a 100644
--- a/src/ptbench/data/hivtb/fold_4.py
+++ b/src/ptbench/config/data/hivtb/fold_4.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/data/hivtb/fold_5.py b/src/ptbench/config/data/hivtb/fold_5.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_5.py
rename to src/ptbench/config/data/hivtb/fold_5.py
index 03170e28..e06f9dd1 100644
--- a/src/ptbench/data/hivtb/fold_5.py
+++ b/src/ptbench/config/data/hivtb/fold_5.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/data/hivtb/fold_6.py b/src/ptbench/config/data/hivtb/fold_6.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_6.py
rename to src/ptbench/config/data/hivtb/fold_6.py
index 9950b0df..4b7db6de 100644
--- a/src/ptbench/data/hivtb/fold_6.py
+++ b/src/ptbench/config/data/hivtb/fold_6.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/data/hivtb/fold_7.py b/src/ptbench/config/data/hivtb/fold_7.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_7.py
rename to src/ptbench/config/data/hivtb/fold_7.py
index 043ef9de..3670047c 100644
--- a/src/ptbench/data/hivtb/fold_7.py
+++ b/src/ptbench/config/data/hivtb/fold_7.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/data/hivtb/fold_8.py b/src/ptbench/config/data/hivtb/fold_8.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_8.py
rename to src/ptbench/config/data/hivtb/fold_8.py
index 9aa80c51..c0900d15 100644
--- a/src/ptbench/data/hivtb/fold_8.py
+++ b/src/ptbench/config/data/hivtb/fold_8.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/data/hivtb/fold_9.py b/src/ptbench/config/data/hivtb/fold_9.py
similarity index 65%
rename from src/ptbench/data/hivtb/fold_9.py
rename to src/ptbench/config/data/hivtb/fold_9.py
index 94a38a15..96ceb596 100644
--- a/src/ptbench/data/hivtb/fold_9.py
+++ b/src/ptbench/config/data/hivtb/fold_9.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/data/montgomery/__init__.py b/src/ptbench/config/data/indian/__init__.py
similarity index 100%
rename from src/ptbench/data/montgomery/__init__.py
rename to src/ptbench/config/data/indian/__init__.py
diff --git a/src/ptbench/data/indian/datamodule.py b/src/ptbench/config/data/indian/datamodule.py
similarity index 78%
rename from src/ptbench/data/indian/datamodule.py
rename to src/ptbench/config/data/indian/datamodule.py
index a17a0bef..1c514f47 100644
--- a/src/ptbench/data/indian/datamodule.py
+++ b/src/ptbench/config/data/indian/datamodule.py
@@ -8,10 +8,14 @@ Database reference: [INDIAN-2013]_
import importlib.resources
-from ..datamodule import CachingDataModule
-from ..shenzhen.datamodule import RawDataLoader
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
def make_split(basename: str) -> DatabaseSplit:
@@ -60,5 +64,7 @@ class DataModule(CachingDataModule):
def __init__(self, split_filename: str):
super().__init__(
database_split=make_split(split_filename),
- raw_data_loader=RawDataLoader(config_variable="datadir.indian"),
+ raw_data_loader=RawDataLoader(
+ config_variable=CONFIGURATION_KEY_DATADIR
+ ),
)
diff --git a/src/ptbench/data/indian/default.json b/src/ptbench/config/data/indian/default.json
similarity index 100%
rename from src/ptbench/data/indian/default.json
rename to src/ptbench/config/data/indian/default.json
diff --git a/src/ptbench/data/indian/default.py b/src/ptbench/config/data/indian/default.py
similarity index 65%
rename from src/ptbench/data/indian/default.py
rename to src/ptbench/config/data/indian/default.py
index cd5c98bf..33bcb48d 100644
--- a/src/ptbench/data/indian/default.py
+++ b/src/ptbench/config/data/indian/default.py
@@ -5,9 +5,9 @@
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/data/indian/fold-0.json b/src/ptbench/config/data/indian/fold-0.json
similarity index 100%
rename from src/ptbench/data/indian/fold-0.json
rename to src/ptbench/config/data/indian/fold-0.json
diff --git a/src/ptbench/data/indian/fold-1.json b/src/ptbench/config/data/indian/fold-1.json
similarity index 100%
rename from src/ptbench/data/indian/fold-1.json
rename to src/ptbench/config/data/indian/fold-1.json
diff --git a/src/ptbench/data/indian/fold-2.json b/src/ptbench/config/data/indian/fold-2.json
similarity index 100%
rename from src/ptbench/data/indian/fold-2.json
rename to src/ptbench/config/data/indian/fold-2.json
diff --git a/src/ptbench/data/indian/fold-3.json b/src/ptbench/config/data/indian/fold-3.json
similarity index 100%
rename from src/ptbench/data/indian/fold-3.json
rename to src/ptbench/config/data/indian/fold-3.json
diff --git a/src/ptbench/data/indian/fold-4.json b/src/ptbench/config/data/indian/fold-4.json
similarity index 100%
rename from src/ptbench/data/indian/fold-4.json
rename to src/ptbench/config/data/indian/fold-4.json
diff --git a/src/ptbench/data/indian/fold-5.json b/src/ptbench/config/data/indian/fold-5.json
similarity index 100%
rename from src/ptbench/data/indian/fold-5.json
rename to src/ptbench/config/data/indian/fold-5.json
diff --git a/src/ptbench/data/indian/fold-6.json b/src/ptbench/config/data/indian/fold-6.json
similarity index 100%
rename from src/ptbench/data/indian/fold-6.json
rename to src/ptbench/config/data/indian/fold-6.json
diff --git a/src/ptbench/data/indian/fold-7.json b/src/ptbench/config/data/indian/fold-7.json
similarity index 100%
rename from src/ptbench/data/indian/fold-7.json
rename to src/ptbench/config/data/indian/fold-7.json
diff --git a/src/ptbench/data/indian/fold-8.json b/src/ptbench/config/data/indian/fold-8.json
similarity index 100%
rename from src/ptbench/data/indian/fold-8.json
rename to src/ptbench/config/data/indian/fold-8.json
diff --git a/src/ptbench/data/indian/fold-9.json b/src/ptbench/config/data/indian/fold-9.json
similarity index 100%
rename from src/ptbench/data/indian/fold-9.json
rename to src/ptbench/config/data/indian/fold-9.json
diff --git a/src/ptbench/data/indian/fold_0.py b/src/ptbench/config/data/indian/fold_0.py
similarity index 66%
rename from src/ptbench/data/indian/fold_0.py
rename to src/ptbench/config/data/indian/fold_0.py
index e316888d..6a8e6c5b 100644
--- a/src/ptbench/data/indian/fold_0.py
+++ b/src/ptbench/config/data/indian/fold_0.py
@@ -6,9 +6,9 @@ fold 0).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/data/indian/fold_1.py b/src/ptbench/config/data/indian/fold_1.py
similarity index 66%
rename from src/ptbench/data/indian/fold_1.py
rename to src/ptbench/config/data/indian/fold_1.py
index 000a8410..029b6df6 100644
--- a/src/ptbench/data/indian/fold_1.py
+++ b/src/ptbench/config/data/indian/fold_1.py
@@ -6,9 +6,9 @@ fold 1).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/data/indian/fold_2.py b/src/ptbench/config/data/indian/fold_2.py
similarity index 66%
rename from src/ptbench/data/indian/fold_2.py
rename to src/ptbench/config/data/indian/fold_2.py
index 9f9152b3..f54f35e5 100644
--- a/src/ptbench/data/indian/fold_2.py
+++ b/src/ptbench/config/data/indian/fold_2.py
@@ -6,9 +6,9 @@ fold 2).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/data/indian/fold_3.py b/src/ptbench/config/data/indian/fold_3.py
similarity index 66%
rename from src/ptbench/data/indian/fold_3.py
rename to src/ptbench/config/data/indian/fold_3.py
index 16475b98..0c493592 100644
--- a/src/ptbench/data/indian/fold_3.py
+++ b/src/ptbench/config/data/indian/fold_3.py
@@ -6,9 +6,9 @@ fold 3).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/data/indian/fold_4.py b/src/ptbench/config/data/indian/fold_4.py
similarity index 66%
rename from src/ptbench/data/indian/fold_4.py
rename to src/ptbench/config/data/indian/fold_4.py
index e2844b97..52a7b792 100644
--- a/src/ptbench/data/indian/fold_4.py
+++ b/src/ptbench/config/data/indian/fold_4.py
@@ -6,9 +6,9 @@ fold 4).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/data/indian/fold_5.py b/src/ptbench/config/data/indian/fold_5.py
similarity index 66%
rename from src/ptbench/data/indian/fold_5.py
rename to src/ptbench/config/data/indian/fold_5.py
index ef583528..843a1e8c 100644
--- a/src/ptbench/data/indian/fold_5.py
+++ b/src/ptbench/config/data/indian/fold_5.py
@@ -6,9 +6,9 @@ fold 5).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/data/indian/fold_6.py b/src/ptbench/config/data/indian/fold_6.py
similarity index 66%
rename from src/ptbench/data/indian/fold_6.py
rename to src/ptbench/config/data/indian/fold_6.py
index 59c168c5..9970d6f6 100644
--- a/src/ptbench/data/indian/fold_6.py
+++ b/src/ptbench/config/data/indian/fold_6.py
@@ -6,9 +6,9 @@ fold 6).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/data/indian/fold_7.py b/src/ptbench/config/data/indian/fold_7.py
similarity index 66%
rename from src/ptbench/data/indian/fold_7.py
rename to src/ptbench/config/data/indian/fold_7.py
index 9eda09ad..5bbef8db 100644
--- a/src/ptbench/data/indian/fold_7.py
+++ b/src/ptbench/config/data/indian/fold_7.py
@@ -6,9 +6,9 @@ fold 7).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/data/indian/fold_8.py b/src/ptbench/config/data/indian/fold_8.py
similarity index 66%
rename from src/ptbench/data/indian/fold_8.py
rename to src/ptbench/config/data/indian/fold_8.py
index abc54bac..0416153f 100644
--- a/src/ptbench/data/indian/fold_8.py
+++ b/src/ptbench/config/data/indian/fold_8.py
@@ -6,9 +6,9 @@ fold 8).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/data/indian/fold_9.py b/src/ptbench/config/data/indian/fold_9.py
similarity index 66%
rename from src/ptbench/data/indian/fold_9.py
rename to src/ptbench/config/data/indian/fold_9.py
index cb4aa6be..3d4df2a5 100644
--- a/src/ptbench/data/indian/fold_9.py
+++ b/src/ptbench/config/data/indian/fold_9.py
@@ -6,9 +6,9 @@ fold 9).
Database reference: [INDIAN-2013]_
-See :py:class:`.indian.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/data/montgomery_shenzhen/__init__.py b/src/ptbench/config/data/montgomery/__init__.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/__init__.py
rename to src/ptbench/config/data/montgomery/__init__.py
diff --git a/src/ptbench/data/montgomery/datamodule.py b/src/ptbench/config/data/montgomery/datamodule.py
similarity index 86%
rename from src/ptbench/data/montgomery/datamodule.py
rename to src/ptbench/config/data/montgomery/datamodule.py
index b5ed48dd..84cdbc77 100644
--- a/src/ptbench/data/montgomery/datamodule.py
+++ b/src/ptbench/config/data/montgomery/datamodule.py
@@ -13,13 +13,17 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..image_utils import remove_black_borders
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
class RawDataLoader(_BaseRawDataLoader):
@@ -31,7 +35,7 @@ class RawDataLoader(_BaseRawDataLoader):
def __init__(self):
self.datadir = load_rc().get(
- "datadir.montgomery", os.path.realpath(os.curdir)
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
)
def sample(self, sample: tuple[str, int]) -> Sample:
diff --git a/src/ptbench/data/montgomery/default.json b/src/ptbench/config/data/montgomery/default.json
similarity index 100%
rename from src/ptbench/data/montgomery/default.json
rename to src/ptbench/config/data/montgomery/default.json
diff --git a/src/ptbench/data/montgomery/default.py b/src/ptbench/config/data/montgomery/default.py
similarity index 63%
rename from src/ptbench/data/montgomery/default.py
rename to src/ptbench/config/data/montgomery/default.py
index ad32e45b..fa890210 100644
--- a/src/ptbench/data/montgomery/default.py
+++ b/src/ptbench/config/data/montgomery/default.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/data/montgomery/fold-0.json b/src/ptbench/config/data/montgomery/fold-0.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-0.json
rename to src/ptbench/config/data/montgomery/fold-0.json
diff --git a/src/ptbench/data/montgomery/fold-1.json b/src/ptbench/config/data/montgomery/fold-1.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-1.json
rename to src/ptbench/config/data/montgomery/fold-1.json
diff --git a/src/ptbench/data/montgomery/fold-2.json b/src/ptbench/config/data/montgomery/fold-2.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-2.json
rename to src/ptbench/config/data/montgomery/fold-2.json
diff --git a/src/ptbench/data/montgomery/fold-3.json b/src/ptbench/config/data/montgomery/fold-3.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-3.json
rename to src/ptbench/config/data/montgomery/fold-3.json
diff --git a/src/ptbench/data/montgomery/fold-4.json b/src/ptbench/config/data/montgomery/fold-4.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-4.json
rename to src/ptbench/config/data/montgomery/fold-4.json
diff --git a/src/ptbench/data/montgomery/fold-5.json b/src/ptbench/config/data/montgomery/fold-5.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-5.json
rename to src/ptbench/config/data/montgomery/fold-5.json
diff --git a/src/ptbench/data/montgomery/fold-6.json b/src/ptbench/config/data/montgomery/fold-6.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-6.json
rename to src/ptbench/config/data/montgomery/fold-6.json
diff --git a/src/ptbench/data/montgomery/fold-7.json b/src/ptbench/config/data/montgomery/fold-7.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-7.json
rename to src/ptbench/config/data/montgomery/fold-7.json
diff --git a/src/ptbench/data/montgomery/fold-8.json b/src/ptbench/config/data/montgomery/fold-8.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-8.json
rename to src/ptbench/config/data/montgomery/fold-8.json
diff --git a/src/ptbench/data/montgomery/fold-9.json b/src/ptbench/config/data/montgomery/fold-9.json
similarity index 100%
rename from src/ptbench/data/montgomery/fold-9.json
rename to src/ptbench/config/data/montgomery/fold-9.json
diff --git a/src/ptbench/data/montgomery/fold_0.py b/src/ptbench/config/data/montgomery/fold_0.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_0.py
rename to src/ptbench/config/data/montgomery/fold_0.py
index 7f842d59..2f72873e 100644
--- a/src/ptbench/data/montgomery/fold_0.py
+++ b/src/ptbench/config/data/montgomery/fold_0.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/data/montgomery/fold_1.py b/src/ptbench/config/data/montgomery/fold_1.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_1.py
rename to src/ptbench/config/data/montgomery/fold_1.py
index abdfbcf1..e4fd9fe8 100644
--- a/src/ptbench/data/montgomery/fold_1.py
+++ b/src/ptbench/config/data/montgomery/fold_1.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/data/montgomery/fold_2.py b/src/ptbench/config/data/montgomery/fold_2.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_2.py
rename to src/ptbench/config/data/montgomery/fold_2.py
index 8614cc00..903154be 100644
--- a/src/ptbench/data/montgomery/fold_2.py
+++ b/src/ptbench/config/data/montgomery/fold_2.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/data/montgomery/fold_3.py b/src/ptbench/config/data/montgomery/fold_3.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_3.py
rename to src/ptbench/config/data/montgomery/fold_3.py
index 50ac23f5..27d9ebdd 100644
--- a/src/ptbench/data/montgomery/fold_3.py
+++ b/src/ptbench/config/data/montgomery/fold_3.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/data/montgomery/fold_4.py b/src/ptbench/config/data/montgomery/fold_4.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_4.py
rename to src/ptbench/config/data/montgomery/fold_4.py
index c83e1060..e5379102 100644
--- a/src/ptbench/data/montgomery/fold_4.py
+++ b/src/ptbench/config/data/montgomery/fold_4.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/data/montgomery/fold_5.py b/src/ptbench/config/data/montgomery/fold_5.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_5.py
rename to src/ptbench/config/data/montgomery/fold_5.py
index 30b97b03..feb8ac45 100644
--- a/src/ptbench/data/montgomery/fold_5.py
+++ b/src/ptbench/config/data/montgomery/fold_5.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/data/montgomery/fold_6.py b/src/ptbench/config/data/montgomery/fold_6.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_6.py
rename to src/ptbench/config/data/montgomery/fold_6.py
index 86e35ca5..e868c726 100644
--- a/src/ptbench/data/montgomery/fold_6.py
+++ b/src/ptbench/config/data/montgomery/fold_6.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/data/montgomery/fold_7.py b/src/ptbench/config/data/montgomery/fold_7.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_7.py
rename to src/ptbench/config/data/montgomery/fold_7.py
index 9f0bd3da..0415dfba 100644
--- a/src/ptbench/data/montgomery/fold_7.py
+++ b/src/ptbench/config/data/montgomery/fold_7.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/data/montgomery/fold_8.py b/src/ptbench/config/data/montgomery/fold_8.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_8.py
rename to src/ptbench/config/data/montgomery/fold_8.py
index 5ea2dfc9..d00595b0 100644
--- a/src/ptbench/data/montgomery/fold_8.py
+++ b/src/ptbench/config/data/montgomery/fold_8.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/data/montgomery/fold_9.py b/src/ptbench/config/data/montgomery/fold_9.py
similarity index 65%
rename from src/ptbench/data/montgomery/fold_9.py
rename to src/ptbench/config/data/montgomery/fold_9.py
index 41025b73..c9158fd1 100644
--- a/src/ptbench/data/montgomery/fold_9.py
+++ b/src/ptbench/config/data/montgomery/fold_9.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.montgomery.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/__init__.py b/src/ptbench/config/data/montgomery_shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/__init__.py
rename to src/ptbench/config/data/montgomery_shenzhen/__init__.py
diff --git a/src/ptbench/data/montgomery_shenzhen/datamodule.py b/src/ptbench/config/data/montgomery_shenzhen/datamodule.py
similarity index 96%
rename from src/ptbench/data/montgomery_shenzhen/datamodule.py
rename to src/ptbench/config/data/montgomery_shenzhen/datamodule.py
index e1173824..0509dd5f 100644
--- a/src/ptbench/data/montgomery_shenzhen/datamodule.py
+++ b/src/ptbench/config/data/montgomery_shenzhen/datamodule.py
@@ -2,7 +2,8 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ..datamodule import ConcatDataModule
+from ptbench.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/data/montgomery_shenzhen/default.py b/src/ptbench/config/data/montgomery_shenzhen/default.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/default.py
rename to src/ptbench/config/data/montgomery_shenzhen/default.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_0.py b/src/ptbench/config/data/montgomery_shenzhen/fold_0.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_0.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_0.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_1.py b/src/ptbench/config/data/montgomery_shenzhen/fold_1.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_1.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_1.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_2.py b/src/ptbench/config/data/montgomery_shenzhen/fold_2.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_2.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_2.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_3.py b/src/ptbench/config/data/montgomery_shenzhen/fold_3.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_3.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_3.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_4.py b/src/ptbench/config/data/montgomery_shenzhen/fold_4.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_4.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_4.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_5.py b/src/ptbench/config/data/montgomery_shenzhen/fold_5.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_5.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_5.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_6.py b/src/ptbench/config/data/montgomery_shenzhen/fold_6.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_6.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_6.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_7.py b/src/ptbench/config/data/montgomery_shenzhen/fold_7.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_7.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_7.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_8.py b/src/ptbench/config/data/montgomery_shenzhen/fold_8.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_8.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_8.py
diff --git a/src/ptbench/data/montgomery_shenzhen/fold_9.py b/src/ptbench/config/data/montgomery_shenzhen/fold_9.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen/fold_9.py
rename to src/ptbench/config/data/montgomery_shenzhen/fold_9.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_padchest/__init__.py b/src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_padchest/__init__.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/datamodule.py b/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
similarity index 70%
rename from src/ptbench/data/montgomery_shenzhen_indian/datamodule.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
index 6df9a850..0bbb2c3d 100644
--- a/src/ptbench/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -4,13 +4,23 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian
datasets."""
-from ..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 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
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/default.py b/src/ptbench/config/data/montgomery_shenzhen_indian/default.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/default.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/default.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_0.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_0.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_1.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_1.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_2.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_2.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_3.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_3.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_4.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_4.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_5.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_5.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_6.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_6.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_7.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_7.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_8.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_8.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian/fold_9.py b/src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian/fold_9.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/__init__.py b/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/__init__.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
similarity index 70%
rename from src/ptbench/data/montgomery_shenzhen_indian_padchest/datamodule.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index b4317ac4..93d0193f 100644
--- a/src/ptbench/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -4,15 +4,29 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and PadChest
datasets."""
-from ..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
+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
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_padchest/default.py b/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_padchest/default.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
diff --git a/src/ptbench/data/nih_cxr14/__init__.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/data/nih_cxr14/__init__.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
similarity index 69%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index 6f7ee8bc..97615574 100644
--- a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -4,15 +4,27 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets."""
-from ..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
+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
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
diff --git a/src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py b/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
similarity index 100%
rename from src/ptbench/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
rename to src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
diff --git a/src/ptbench/data/nih_cxr14_padchest/__init__.py b/src/ptbench/config/data/nih_cxr14/__init__.py
similarity index 100%
rename from src/ptbench/data/nih_cxr14_padchest/__init__.py
rename to src/ptbench/config/data/nih_cxr14/__init__.py
diff --git a/src/ptbench/data/nih_cxr14/cardiomegaly.json b/src/ptbench/config/data/nih_cxr14/cardiomegaly.json
similarity index 100%
rename from src/ptbench/data/nih_cxr14/cardiomegaly.json
rename to src/ptbench/config/data/nih_cxr14/cardiomegaly.json
diff --git a/src/ptbench/data/nih_cxr14/cardiomegaly.py b/src/ptbench/config/data/nih_cxr14/cardiomegaly.py
similarity index 71%
rename from src/ptbench/data/nih_cxr14/cardiomegaly.py
rename to src/ptbench/config/data/nih_cxr14/cardiomegaly.py
index 7b104faa..77248a47 100644
--- a/src/ptbench/data/nih_cxr14/cardiomegaly.py
+++ b/src/ptbench/config/data/nih_cxr14/cardiomegaly.py
@@ -8,9 +8,10 @@ Database reference: [NIH-CXR14-2017]_
This split contains cardiomegaly cases from the NIH CXR14 database.
-See :py:class:`.nih_cxr14.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("cardiomegaly.json")
diff --git a/src/ptbench/data/nih_cxr14/datamodule.py b/src/ptbench/config/data/nih_cxr14/datamodule.py
similarity index 82%
rename from src/ptbench/data/nih_cxr14/datamodule.py
rename to src/ptbench/config/data/nih_cxr14/datamodule.py
index 996c9feb..9875985f 100644
--- a/src/ptbench/data/nih_cxr14/datamodule.py
+++ b/src/ptbench/config/data/nih_cxr14/datamodule.py
@@ -13,12 +13,27 @@ import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
+
+CONFIGURATION_KEY_IDIAP_FILESTRUCTURE = (
+ __name__.rsplit(".", 2)[-2]
+) + ".idiap_folder_structure"
+"""Key to search for in the configuration file indicating if the loader should
+use standard or idiap-based file organisation structure.
+
+It causes the internal loader to search for files in a slightly
+different folder structure, that was adapted to Idiap's requirements
+(number of files per folder to be less than 10k).
+"""
class RawDataLoader(_BaseRawDataLoader):
@@ -40,9 +55,11 @@ class RawDataLoader(_BaseRawDataLoader):
def __init__(self):
rc = load_rc()
- self.datadir = rc.get("datadir.nih_cxr14", os.path.realpath(os.curdir))
+ self.datadir = rc.get(
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
+ )
self.idiap_file_organisation = rc.get(
- "nih_cxr14.idiap_folder_structure", False
+ CONFIGURATION_KEY_IDIAP_FILESTRUCTURE, False
)
def sample(self, sample: tuple[str, list[int]]) -> Sample:
diff --git a/src/ptbench/data/nih_cxr14/default.json.bz2 b/src/ptbench/config/data/nih_cxr14/default.json.bz2
similarity index 100%
rename from src/ptbench/data/nih_cxr14/default.json.bz2
rename to src/ptbench/config/data/nih_cxr14/default.json.bz2
diff --git a/src/ptbench/data/nih_cxr14/default.py b/src/ptbench/config/data/nih_cxr14/default.py
similarity index 67%
rename from src/ptbench/data/nih_cxr14/default.py
rename to src/ptbench/config/data/nih_cxr14/default.py
index c7bc3e2e..00ac5afd 100644
--- a/src/ptbench/data/nih_cxr14/default.py
+++ b/src/ptbench/config/data/nih_cxr14/default.py
@@ -7,9 +7,10 @@
* Validation samples: 6350
* Test samples: 4054
-See :py:class:`.nih_cxr14.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("default.json.bz2")
diff --git a/src/ptbench/data/padchest/__init__.py b/src/ptbench/config/data/nih_cxr14_padchest/__init__.py
similarity index 100%
rename from src/ptbench/data/padchest/__init__.py
rename to src/ptbench/config/data/nih_cxr14_padchest/__init__.py
diff --git a/src/ptbench/data/nih_cxr14_padchest/datamodule.py b/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
similarity index 73%
rename from src/ptbench/data/nih_cxr14_padchest/datamodule.py
rename to src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
index f1ce1f91..cd2d8fb2 100644
--- a/src/ptbench/data/nih_cxr14_padchest/datamodule.py
+++ b/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
@@ -2,11 +2,19 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ..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
+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
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/data/nih_cxr14_padchest/idiap.py b/src/ptbench/config/data/nih_cxr14_padchest/idiap.py
similarity index 100%
rename from src/ptbench/data/nih_cxr14_padchest/idiap.py
rename to src/ptbench/config/data/nih_cxr14_padchest/idiap.py
diff --git a/src/ptbench/data/shenzhen/__init__.py b/src/ptbench/config/data/padchest/__init__.py
similarity index 100%
rename from src/ptbench/data/shenzhen/__init__.py
rename to src/ptbench/config/data/padchest/__init__.py
diff --git a/src/ptbench/data/padchest/cardiomegaly-idiap.json b/src/ptbench/config/data/padchest/cardiomegaly-idiap.json
similarity index 100%
rename from src/ptbench/data/padchest/cardiomegaly-idiap.json
rename to src/ptbench/config/data/padchest/cardiomegaly-idiap.json
diff --git a/src/ptbench/data/padchest/cardiomegaly_idiap.py b/src/ptbench/config/data/padchest/cardiomegaly_idiap.py
similarity index 72%
rename from src/ptbench/data/padchest/cardiomegaly_idiap.py
rename to src/ptbench/config/data/padchest/cardiomegaly_idiap.py
index bd832fdd..a22cdc08 100644
--- a/src/ptbench/data/padchest/cardiomegaly_idiap.py
+++ b/src/ptbench/config/data/padchest/cardiomegaly_idiap.py
@@ -8,9 +8,11 @@ Database reference: [PADCHEST-2019]_
This split contains the first 40 images with cardiomegaly, with parameters:
Label = "Normal", MethodLabel = "Physician", Projection = "PA"
-Read documentation of :py:class:`DataModule` for technical details.
+Read documentation of
+:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.padchest.datamodule import DataModule
datamodule = DataModule("cardiomegaly-idiap.json")
diff --git a/src/ptbench/data/padchest/datamodule.py b/src/ptbench/config/data/padchest/datamodule.py
similarity index 94%
rename from src/ptbench/data/padchest/datamodule.py
rename to src/ptbench/config/data/padchest/datamodule.py
index 1fc49485..0122a429 100644
--- a/src/ptbench/data/padchest/datamodule.py
+++ b/src/ptbench/config/data/padchest/datamodule.py
@@ -14,13 +14,17 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..image_utils import remove_black_borders
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
class RawDataLoader(_BaseRawDataLoader):
@@ -32,7 +36,9 @@ class RawDataLoader(_BaseRawDataLoader):
def __init__(self):
rc = load_rc()
- self.datadir = rc.get("datadir.padchest", os.path.realpath(os.curdir))
+ self.datadir = rc.get(
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
+ )
def sample(self, sample: tuple[str, int | list[int]]) -> Sample:
"""Loads a single image sample from the disk.
diff --git a/src/ptbench/data/padchest/idiap.json.bz2 b/src/ptbench/config/data/padchest/idiap.json.bz2
similarity index 100%
rename from src/ptbench/data/padchest/idiap.json.bz2
rename to src/ptbench/config/data/padchest/idiap.json.bz2
diff --git a/src/ptbench/data/padchest/idiap.py b/src/ptbench/config/data/padchest/idiap.py
similarity index 67%
rename from src/ptbench/data/padchest/idiap.py
rename to src/ptbench/config/data/padchest/idiap.py
index bf1f9356..be0f9b2f 100644
--- a/src/ptbench/data/padchest/idiap.py
+++ b/src/ptbench/config/data/padchest/idiap.py
@@ -6,14 +6,15 @@
Database reference: [PADCHEST-2019]_
This split contains all images in the database. Read documentation of
-:py:class:`.padchest.datamodule.DataModule` for technical details.
+:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+details.
* Split reference: ours
* Training samples: 96'269
- * Validation samples: ?
- * Test samples: ?
+ * Validation samples: 0
+ * Test samples: 0
"""
-from .datamodule import DataModule
+from ptbench.config.data.padchest.datamodule import DataModule
datamodule = DataModule("idiap.json.bz2")
diff --git a/src/ptbench/data/padchest/no-tb-idiap.json.bz2 b/src/ptbench/config/data/padchest/no-tb-idiap.json.bz2
similarity index 100%
rename from src/ptbench/data/padchest/no-tb-idiap.json.bz2
rename to src/ptbench/config/data/padchest/no-tb-idiap.json.bz2
diff --git a/src/ptbench/data/padchest/no_tb_idiap.py b/src/ptbench/config/data/padchest/no_tb_idiap.py
similarity index 81%
rename from src/ptbench/data/padchest/no_tb_idiap.py
rename to src/ptbench/config/data/padchest/no_tb_idiap.py
index ca787520..8c2c5fc7 100644
--- a/src/ptbench/data/padchest/no_tb_idiap.py
+++ b/src/ptbench/config/data/padchest/no_tb_idiap.py
@@ -28,10 +28,11 @@ Database reference: [PADCHEST-2019]_
* fibrosis
* edema and consolidation
-Read documentation of :py:class:`.padchest.datamodule.DataModule` for technical
+Read documentation of
+:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.padchest.datamodule import DataModule
datamodule = DataModule("no-tb-idiap.json.bz2")
diff --git a/src/ptbench/data/padchest/tb-idiap.json b/src/ptbench/config/data/padchest/tb-idiap.json
similarity index 100%
rename from src/ptbench/data/padchest/tb-idiap.json
rename to src/ptbench/config/data/padchest/tb-idiap.json
diff --git a/src/ptbench/data/padchest/tb_idiap.py b/src/ptbench/config/data/padchest/tb_idiap.py
similarity index 77%
rename from src/ptbench/data/padchest/tb_idiap.py
rename to src/ptbench/config/data/padchest/tb_idiap.py
index d77e5afd..c6c4da93 100644
--- a/src/ptbench/data/padchest/tb_idiap.py
+++ b/src/ptbench/config/data/padchest/tb_idiap.py
@@ -10,10 +10,11 @@ the following parameters: Label = "Normal", MethodLabel = "Physician",
Projection = "PA" and TB cases. Labelling matches those for active TB (binary)
classification datasets.
-Read documentation of :py:class:`.padchest.datamodule.DataModule` for technical
+Read documentation of
+:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.padchest.datamodule import DataModule
datamodule = DataModule("tb-idiap.json")
diff --git a/src/ptbench/data/tbpoc/__init__.py b/src/ptbench/config/data/shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/data/tbpoc/__init__.py
rename to src/ptbench/config/data/shenzhen/__init__.py
diff --git a/src/ptbench/data/shenzhen/datamodule.py b/src/ptbench/config/data/shenzhen/datamodule.py
similarity index 84%
rename from src/ptbench/data/shenzhen/datamodule.py
rename to src/ptbench/config/data/shenzhen/datamodule.py
index af5a4074..70c63893 100644
--- a/src/ptbench/data/shenzhen/datamodule.py
+++ b/src/ptbench/config/data/shenzhen/datamodule.py
@@ -13,13 +13,17 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..image_utils import remove_black_borders
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
class RawDataLoader(_BaseRawDataLoader):
@@ -29,7 +33,9 @@ class RawDataLoader(_BaseRawDataLoader):
"""This variable contains the base directory where the database raw data is
stored."""
- def __init__(self, config_variable: str = "datadir.shenzhen"):
+ # config_variable: required so this loader can be used for the Indian
+ # database as well.
+ def __init__(self, config_variable: str = CONFIGURATION_KEY_DATADIR):
self.datadir = load_rc().get(
config_variable, os.path.realpath(os.curdir)
)
diff --git a/src/ptbench/data/shenzhen/default.json b/src/ptbench/config/data/shenzhen/default.json
similarity index 100%
rename from src/ptbench/data/shenzhen/default.json
rename to src/ptbench/config/data/shenzhen/default.json
diff --git a/src/ptbench/data/shenzhen/default.py b/src/ptbench/config/data/shenzhen/default.py
similarity index 75%
rename from src/ptbench/data/shenzhen/default.py
rename to src/ptbench/config/data/shenzhen/default.py
index b8cf7172..fd0dbaf1 100644
--- a/src/ptbench/data/shenzhen/default.py
+++ b/src/ptbench/config/data/shenzhen/default.py
@@ -9,9 +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:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/data/shenzhen/fold-0.json b/src/ptbench/config/data/shenzhen/fold-0.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-0.json
rename to src/ptbench/config/data/shenzhen/fold-0.json
diff --git a/src/ptbench/data/shenzhen/fold-1.json b/src/ptbench/config/data/shenzhen/fold-1.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-1.json
rename to src/ptbench/config/data/shenzhen/fold-1.json
diff --git a/src/ptbench/data/shenzhen/fold-2.json b/src/ptbench/config/data/shenzhen/fold-2.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-2.json
rename to src/ptbench/config/data/shenzhen/fold-2.json
diff --git a/src/ptbench/data/shenzhen/fold-3.json b/src/ptbench/config/data/shenzhen/fold-3.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-3.json
rename to src/ptbench/config/data/shenzhen/fold-3.json
diff --git a/src/ptbench/data/shenzhen/fold-4.json b/src/ptbench/config/data/shenzhen/fold-4.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-4.json
rename to src/ptbench/config/data/shenzhen/fold-4.json
diff --git a/src/ptbench/data/shenzhen/fold-5.json b/src/ptbench/config/data/shenzhen/fold-5.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-5.json
rename to src/ptbench/config/data/shenzhen/fold-5.json
diff --git a/src/ptbench/data/shenzhen/fold-6.json b/src/ptbench/config/data/shenzhen/fold-6.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-6.json
rename to src/ptbench/config/data/shenzhen/fold-6.json
diff --git a/src/ptbench/data/shenzhen/fold-7.json b/src/ptbench/config/data/shenzhen/fold-7.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-7.json
rename to src/ptbench/config/data/shenzhen/fold-7.json
diff --git a/src/ptbench/data/shenzhen/fold-8.json b/src/ptbench/config/data/shenzhen/fold-8.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-8.json
rename to src/ptbench/config/data/shenzhen/fold-8.json
diff --git a/src/ptbench/data/shenzhen/fold-9.json b/src/ptbench/config/data/shenzhen/fold-9.json
similarity index 100%
rename from src/ptbench/data/shenzhen/fold-9.json
rename to src/ptbench/config/data/shenzhen/fold-9.json
diff --git a/src/ptbench/data/shenzhen/fold_0.py b/src/ptbench/config/data/shenzhen/fold_0.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_0.py
rename to src/ptbench/config/data/shenzhen/fold_0.py
index df1359ae..890250db 100644
--- a/src/ptbench/data/shenzhen/fold_0.py
+++ b/src/ptbench/config/data/shenzhen/fold_0.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/data/shenzhen/fold_1.py b/src/ptbench/config/data/shenzhen/fold_1.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_1.py
rename to src/ptbench/config/data/shenzhen/fold_1.py
index 03be3fa6..ff95e0d0 100644
--- a/src/ptbench/data/shenzhen/fold_1.py
+++ b/src/ptbench/config/data/shenzhen/fold_1.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/data/shenzhen/fold_2.py b/src/ptbench/config/data/shenzhen/fold_2.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_2.py
rename to src/ptbench/config/data/shenzhen/fold_2.py
index f4bd72d8..db16495c 100644
--- a/src/ptbench/data/shenzhen/fold_2.py
+++ b/src/ptbench/config/data/shenzhen/fold_2.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/data/shenzhen/fold_3.py b/src/ptbench/config/data/shenzhen/fold_3.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_3.py
rename to src/ptbench/config/data/shenzhen/fold_3.py
index b41c7886..d0321c86 100644
--- a/src/ptbench/data/shenzhen/fold_3.py
+++ b/src/ptbench/config/data/shenzhen/fold_3.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/data/shenzhen/fold_4.py b/src/ptbench/config/data/shenzhen/fold_4.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_4.py
rename to src/ptbench/config/data/shenzhen/fold_4.py
index f9105989..f6760358 100644
--- a/src/ptbench/data/shenzhen/fold_4.py
+++ b/src/ptbench/config/data/shenzhen/fold_4.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/data/shenzhen/fold_5.py b/src/ptbench/config/data/shenzhen/fold_5.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_5.py
rename to src/ptbench/config/data/shenzhen/fold_5.py
index 7882e899..6d77a840 100644
--- a/src/ptbench/data/shenzhen/fold_5.py
+++ b/src/ptbench/config/data/shenzhen/fold_5.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/data/shenzhen/fold_6.py b/src/ptbench/config/data/shenzhen/fold_6.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_6.py
rename to src/ptbench/config/data/shenzhen/fold_6.py
index 4d11aca0..3ecd646e 100644
--- a/src/ptbench/data/shenzhen/fold_6.py
+++ b/src/ptbench/config/data/shenzhen/fold_6.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/data/shenzhen/fold_7.py b/src/ptbench/config/data/shenzhen/fold_7.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_7.py
rename to src/ptbench/config/data/shenzhen/fold_7.py
index 8a794345..61ba5d27 100644
--- a/src/ptbench/data/shenzhen/fold_7.py
+++ b/src/ptbench/config/data/shenzhen/fold_7.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/data/shenzhen/fold_8.py b/src/ptbench/config/data/shenzhen/fold_8.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_8.py
rename to src/ptbench/config/data/shenzhen/fold_8.py
index 9abe5fa4..a03121d5 100644
--- a/src/ptbench/data/shenzhen/fold_8.py
+++ b/src/ptbench/config/data/shenzhen/fold_8.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/data/shenzhen/fold_9.py b/src/ptbench/config/data/shenzhen/fold_9.py
similarity index 66%
rename from src/ptbench/data/shenzhen/fold_9.py
rename to src/ptbench/config/data/shenzhen/fold_9.py
index 06fab974..168031c8 100644
--- a/src/ptbench/data/shenzhen/fold_9.py
+++ b/src/ptbench/config/data/shenzhen/fold_9.py
@@ -5,9 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`.shenzhen.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+technical details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/data/tbx11k/__init__.py b/src/ptbench/config/data/tbpoc/__init__.py
similarity index 100%
rename from src/ptbench/data/tbx11k/__init__.py
rename to src/ptbench/config/data/tbpoc/__init__.py
diff --git a/src/ptbench/data/tbpoc/datamodule.py b/src/ptbench/config/data/tbpoc/datamodule.py
similarity index 84%
rename from src/ptbench/data/tbpoc/datamodule.py
rename to src/ptbench/config/data/tbpoc/datamodule.py
index f564e232..42a3a10f 100644
--- a/src/ptbench/data/tbpoc/datamodule.py
+++ b/src/ptbench/config/data/tbpoc/datamodule.py
@@ -9,13 +9,17 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..image_utils import remove_black_borders
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
class RawDataLoader(_BaseRawDataLoader):
@@ -25,9 +29,9 @@ class RawDataLoader(_BaseRawDataLoader):
"""This variable contains the base directory where the database raw data is
stored."""
- def __init__(self, config_variable: str = "datadir.tbpoc"):
+ def __init__(self):
self.datadir = load_rc().get(
- config_variable, os.path.realpath(os.curdir)
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
)
def sample(self, sample: tuple[str, int]) -> Sample:
diff --git a/src/ptbench/data/tbpoc/fold-0.json b/src/ptbench/config/data/tbpoc/fold-0.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-0.json
rename to src/ptbench/config/data/tbpoc/fold-0.json
diff --git a/src/ptbench/data/tbpoc/fold-1.json b/src/ptbench/config/data/tbpoc/fold-1.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-1.json
rename to src/ptbench/config/data/tbpoc/fold-1.json
diff --git a/src/ptbench/data/tbpoc/fold-2.json b/src/ptbench/config/data/tbpoc/fold-2.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-2.json
rename to src/ptbench/config/data/tbpoc/fold-2.json
diff --git a/src/ptbench/data/tbpoc/fold-3.json b/src/ptbench/config/data/tbpoc/fold-3.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-3.json
rename to src/ptbench/config/data/tbpoc/fold-3.json
diff --git a/src/ptbench/data/tbpoc/fold-4.json b/src/ptbench/config/data/tbpoc/fold-4.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-4.json
rename to src/ptbench/config/data/tbpoc/fold-4.json
diff --git a/src/ptbench/data/tbpoc/fold-5.json b/src/ptbench/config/data/tbpoc/fold-5.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-5.json
rename to src/ptbench/config/data/tbpoc/fold-5.json
diff --git a/src/ptbench/data/tbpoc/fold-6.json b/src/ptbench/config/data/tbpoc/fold-6.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-6.json
rename to src/ptbench/config/data/tbpoc/fold-6.json
diff --git a/src/ptbench/data/tbpoc/fold-7.json b/src/ptbench/config/data/tbpoc/fold-7.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-7.json
rename to src/ptbench/config/data/tbpoc/fold-7.json
diff --git a/src/ptbench/data/tbpoc/fold-8.json b/src/ptbench/config/data/tbpoc/fold-8.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-8.json
rename to src/ptbench/config/data/tbpoc/fold-8.json
diff --git a/src/ptbench/data/tbpoc/fold-9.json b/src/ptbench/config/data/tbpoc/fold-9.json
similarity index 100%
rename from src/ptbench/data/tbpoc/fold-9.json
rename to src/ptbench/config/data/tbpoc/fold-9.json
diff --git a/src/ptbench/data/tbpoc/fold_0.py b/src/ptbench/config/data/tbpoc/fold_0.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_0.py
rename to src/ptbench/config/data/tbpoc/fold_0.py
index 5c452504..e3a0d242 100644
--- a/src/ptbench/data/tbpoc/fold_0.py
+++ b/src/ptbench/config/data/tbpoc/fold_0.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/data/tbpoc/fold_1.py b/src/ptbench/config/data/tbpoc/fold_1.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_1.py
rename to src/ptbench/config/data/tbpoc/fold_1.py
index a2fe6083..b6a04095 100644
--- a/src/ptbench/data/tbpoc/fold_1.py
+++ b/src/ptbench/config/data/tbpoc/fold_1.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/data/tbpoc/fold_2.py b/src/ptbench/config/data/tbpoc/fold_2.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_2.py
rename to src/ptbench/config/data/tbpoc/fold_2.py
index f0aa508c..c821f0cc 100644
--- a/src/ptbench/data/tbpoc/fold_2.py
+++ b/src/ptbench/config/data/tbpoc/fold_2.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/data/tbpoc/fold_3.py b/src/ptbench/config/data/tbpoc/fold_3.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_3.py
rename to src/ptbench/config/data/tbpoc/fold_3.py
index b13213c7..c5c9fa7d 100644
--- a/src/ptbench/data/tbpoc/fold_3.py
+++ b/src/ptbench/config/data/tbpoc/fold_3.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/data/tbpoc/fold_4.py b/src/ptbench/config/data/tbpoc/fold_4.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_4.py
rename to src/ptbench/config/data/tbpoc/fold_4.py
index fe153fc6..9b3b74d9 100644
--- a/src/ptbench/data/tbpoc/fold_4.py
+++ b/src/ptbench/config/data/tbpoc/fold_4.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/data/tbpoc/fold_5.py b/src/ptbench/config/data/tbpoc/fold_5.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_5.py
rename to src/ptbench/config/data/tbpoc/fold_5.py
index 7759ccc7..7a9947dc 100644
--- a/src/ptbench/data/tbpoc/fold_5.py
+++ b/src/ptbench/config/data/tbpoc/fold_5.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/data/tbpoc/fold_6.py b/src/ptbench/config/data/tbpoc/fold_6.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_6.py
rename to src/ptbench/config/data/tbpoc/fold_6.py
index 35be05a4..0e6a7349 100644
--- a/src/ptbench/data/tbpoc/fold_6.py
+++ b/src/ptbench/config/data/tbpoc/fold_6.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/data/tbpoc/fold_7.py b/src/ptbench/config/data/tbpoc/fold_7.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_7.py
rename to src/ptbench/config/data/tbpoc/fold_7.py
index da5bec1e..bb257c8e 100644
--- a/src/ptbench/data/tbpoc/fold_7.py
+++ b/src/ptbench/config/data/tbpoc/fold_7.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/data/tbpoc/fold_8.py b/src/ptbench/config/data/tbpoc/fold_8.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_8.py
rename to src/ptbench/config/data/tbpoc/fold_8.py
index 65339cc0..790f13c9 100644
--- a/src/ptbench/data/tbpoc/fold_8.py
+++ b/src/ptbench/config/data/tbpoc/fold_8.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/data/tbpoc/fold_9.py b/src/ptbench/config/data/tbpoc/fold_9.py
similarity index 65%
rename from src/ptbench/data/tbpoc/fold_9.py
rename to src/ptbench/config/data/tbpoc/fold_9.py
index dd42e068..a53852a6 100644
--- a/src/ptbench/data/tbpoc/fold_9.py
+++ b/src/ptbench/config/data/tbpoc/fold_9.py
@@ -5,9 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`.tbpoc.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/models/config/__init__.py b/src/ptbench/config/data/tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/models/config/__init__.py
rename to src/ptbench/config/data/tbx11k/__init__.py
diff --git a/src/ptbench/data/tbx11k/datamodule.py b/src/ptbench/config/data/tbx11k/datamodule.py
similarity index 93%
rename from src/ptbench/data/tbx11k/datamodule.py
rename to src/ptbench/config/data/tbx11k/datamodule.py
index 45cab752..a5959e82 100644
--- a/src/ptbench/data/tbx11k/datamodule.py
+++ b/src/ptbench/config/data/tbx11k/datamodule.py
@@ -10,12 +10,17 @@ import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ...utils.rc import load_rc
-from ..datamodule import CachingDataModule
-from ..split import JSONDatabaseSplit
-from ..typing import DatabaseSplit
-from ..typing import RawDataLoader as _BaseRawDataLoader
-from ..typing import Sample
+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
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
+
BoundingBoxAnnotation: typing.TypeAlias = tuple[int, int, int, int, int]
"""Location of TB radiological findings (latent or active)
@@ -55,7 +60,7 @@ class RawDataLoader(_BaseRawDataLoader):
def __init__(self):
self.datadir = load_rc().get(
- "datadir.tbx11k", os.path.realpath(os.curdir)
+ CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir)
)
def sample(self, sample: DatabaseSample) -> Sample:
diff --git a/src/ptbench/data/tbx11k/make_splits_from_database.py b/src/ptbench/config/data/tbx11k/make_splits_from_database.py
similarity index 100%
rename from src/ptbench/data/tbx11k/make_splits_from_database.py
rename to src/ptbench/config/data/tbx11k/make_splits_from_database.py
diff --git a/src/ptbench/data/tbx11k/v1-fold-0.json b/src/ptbench/config/data/tbx11k/v1-fold-0.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-0.json
rename to src/ptbench/config/data/tbx11k/v1-fold-0.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-1.json b/src/ptbench/config/data/tbx11k/v1-fold-1.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-1.json
rename to src/ptbench/config/data/tbx11k/v1-fold-1.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-2.json b/src/ptbench/config/data/tbx11k/v1-fold-2.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-2.json
rename to src/ptbench/config/data/tbx11k/v1-fold-2.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-3.json b/src/ptbench/config/data/tbx11k/v1-fold-3.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-3.json
rename to src/ptbench/config/data/tbx11k/v1-fold-3.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-4.json b/src/ptbench/config/data/tbx11k/v1-fold-4.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-4.json
rename to src/ptbench/config/data/tbx11k/v1-fold-4.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-5.json b/src/ptbench/config/data/tbx11k/v1-fold-5.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-5.json
rename to src/ptbench/config/data/tbx11k/v1-fold-5.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-6.json b/src/ptbench/config/data/tbx11k/v1-fold-6.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-6.json
rename to src/ptbench/config/data/tbx11k/v1-fold-6.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-7.json b/src/ptbench/config/data/tbx11k/v1-fold-7.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-7.json
rename to src/ptbench/config/data/tbx11k/v1-fold-7.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-8.json b/src/ptbench/config/data/tbx11k/v1-fold-8.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-8.json
rename to src/ptbench/config/data/tbx11k/v1-fold-8.json
diff --git a/src/ptbench/data/tbx11k/v1-fold-9.json b/src/ptbench/config/data/tbx11k/v1-fold-9.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-fold-9.json
rename to src/ptbench/config/data/tbx11k/v1-fold-9.json
diff --git a/src/ptbench/data/tbx11k/v1-healthy-vs-atb.json b/src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v1-healthy-vs-atb.json
rename to src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json
diff --git a/src/ptbench/data/tbx11k/v1_fold_0.py b/src/ptbench/config/data/tbx11k/v1_fold_0.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_0.py
rename to src/ptbench/config/data/tbx11k/v1_fold_0.py
index ecf1e295..9ba42d52 100644
--- a/src/ptbench/data/tbx11k/v1_fold_0.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_0.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-0.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_1.py b/src/ptbench/config/data/tbx11k/v1_fold_1.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_1.py
rename to src/ptbench/config/data/tbx11k/v1_fold_1.py
index b74f9ac9..ca3fe104 100644
--- a/src/ptbench/data/tbx11k/v1_fold_1.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_1.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-1.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_2.py b/src/ptbench/config/data/tbx11k/v1_fold_2.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_2.py
rename to src/ptbench/config/data/tbx11k/v1_fold_2.py
index c52f415a..c3ec4fe4 100644
--- a/src/ptbench/data/tbx11k/v1_fold_2.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_2.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-2.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_3.py b/src/ptbench/config/data/tbx11k/v1_fold_3.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_3.py
rename to src/ptbench/config/data/tbx11k/v1_fold_3.py
index 32794848..09fb16b2 100644
--- a/src/ptbench/data/tbx11k/v1_fold_3.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_3.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-3.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_4.py b/src/ptbench/config/data/tbx11k/v1_fold_4.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_4.py
rename to src/ptbench/config/data/tbx11k/v1_fold_4.py
index 1c149232..8f96d1e5 100644
--- a/src/ptbench/data/tbx11k/v1_fold_4.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_4.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-4.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_5.py b/src/ptbench/config/data/tbx11k/v1_fold_5.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_5.py
rename to src/ptbench/config/data/tbx11k/v1_fold_5.py
index 2a74b219..8ced06d4 100644
--- a/src/ptbench/data/tbx11k/v1_fold_5.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_5.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-5.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_6.py b/src/ptbench/config/data/tbx11k/v1_fold_6.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_6.py
rename to src/ptbench/config/data/tbx11k/v1_fold_6.py
index 67562a35..28e9f16a 100644
--- a/src/ptbench/data/tbx11k/v1_fold_6.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_6.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-6.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_7.py b/src/ptbench/config/data/tbx11k/v1_fold_7.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_7.py
rename to src/ptbench/config/data/tbx11k/v1_fold_7.py
index 3d80b71e..09886b94 100644
--- a/src/ptbench/data/tbx11k/v1_fold_7.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_7.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-7.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_8.py b/src/ptbench/config/data/tbx11k/v1_fold_8.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_8.py
rename to src/ptbench/config/data/tbx11k/v1_fold_8.py
index f8e45fe1..5fd2dd23 100644
--- a/src/ptbench/data/tbx11k/v1_fold_8.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_8.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-8.json")
diff --git a/src/ptbench/data/tbx11k/v1_fold_9.py b/src/ptbench/config/data/tbx11k/v1_fold_9.py
similarity index 67%
rename from src/ptbench/data/tbx11k/v1_fold_9.py
rename to src/ptbench/config/data/tbx11k/v1_fold_9.py
index 0d394354..440f724f 100644
--- a/src/ptbench/data/tbx11k/v1_fold_9.py
+++ b/src/ptbench/config/data/tbx11k/v1_fold_9.py
@@ -6,9 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-9.json")
diff --git a/src/ptbench/data/tbx11k/v1_healthy_vs_atb.py b/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
similarity index 81%
rename from src/ptbench/data/tbx11k/v1_healthy_vs_atb.py
rename to src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
index 0845f03b..785b6bfb 100644
--- a/src/ptbench/data/tbx11k/v1_healthy_vs_atb.py
+++ b/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
@@ -27,9 +27,10 @@ Split v1 contains healthy subjects against active TB cases (total samples =
- Active TB only: 157
- Total: 957
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-healthy-vs-atb.json")
diff --git a/src/ptbench/data/tbx11k/v2-fold-0.json b/src/ptbench/config/data/tbx11k/v2-fold-0.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-0.json
rename to src/ptbench/config/data/tbx11k/v2-fold-0.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-1.json b/src/ptbench/config/data/tbx11k/v2-fold-1.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-1.json
rename to src/ptbench/config/data/tbx11k/v2-fold-1.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-2.json b/src/ptbench/config/data/tbx11k/v2-fold-2.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-2.json
rename to src/ptbench/config/data/tbx11k/v2-fold-2.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-3.json b/src/ptbench/config/data/tbx11k/v2-fold-3.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-3.json
rename to src/ptbench/config/data/tbx11k/v2-fold-3.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-4.json b/src/ptbench/config/data/tbx11k/v2-fold-4.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-4.json
rename to src/ptbench/config/data/tbx11k/v2-fold-4.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-5.json b/src/ptbench/config/data/tbx11k/v2-fold-5.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-5.json
rename to src/ptbench/config/data/tbx11k/v2-fold-5.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-6.json b/src/ptbench/config/data/tbx11k/v2-fold-6.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-6.json
rename to src/ptbench/config/data/tbx11k/v2-fold-6.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-7.json b/src/ptbench/config/data/tbx11k/v2-fold-7.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-7.json
rename to src/ptbench/config/data/tbx11k/v2-fold-7.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-8.json b/src/ptbench/config/data/tbx11k/v2-fold-8.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-8.json
rename to src/ptbench/config/data/tbx11k/v2-fold-8.json
diff --git a/src/ptbench/data/tbx11k/v2-fold-9.json b/src/ptbench/config/data/tbx11k/v2-fold-9.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-fold-9.json
rename to src/ptbench/config/data/tbx11k/v2-fold-9.json
diff --git a/src/ptbench/data/tbx11k/v2-others-vs-atb.json b/src/ptbench/config/data/tbx11k/v2-others-vs-atb.json
similarity index 100%
rename from src/ptbench/data/tbx11k/v2-others-vs-atb.json
rename to src/ptbench/config/data/tbx11k/v2-others-vs-atb.json
diff --git a/src/ptbench/data/tbx11k/v2_fold_0.py b/src/ptbench/config/data/tbx11k/v2_fold_0.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_0.py
rename to src/ptbench/config/data/tbx11k/v2_fold_0.py
index 8ccb73ed..c713c479 100644
--- a/src/ptbench/data/tbx11k/v2_fold_0.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_0.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-0.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_1.py b/src/ptbench/config/data/tbx11k/v2_fold_1.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_1.py
rename to src/ptbench/config/data/tbx11k/v2_fold_1.py
index 9e1c3aca..10b3b183 100644
--- a/src/ptbench/data/tbx11k/v2_fold_1.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_1.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-1.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_2.py b/src/ptbench/config/data/tbx11k/v2_fold_2.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_2.py
rename to src/ptbench/config/data/tbx11k/v2_fold_2.py
index 24a00ece..f7fd10a6 100644
--- a/src/ptbench/data/tbx11k/v2_fold_2.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_2.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-2.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_3.py b/src/ptbench/config/data/tbx11k/v2_fold_3.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_3.py
rename to src/ptbench/config/data/tbx11k/v2_fold_3.py
index 9da2630d..b744251d 100644
--- a/src/ptbench/data/tbx11k/v2_fold_3.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_3.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-3.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_4.py b/src/ptbench/config/data/tbx11k/v2_fold_4.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_4.py
rename to src/ptbench/config/data/tbx11k/v2_fold_4.py
index 0555b567..17215495 100644
--- a/src/ptbench/data/tbx11k/v2_fold_4.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_4.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-4.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_5.py b/src/ptbench/config/data/tbx11k/v2_fold_5.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_5.py
rename to src/ptbench/config/data/tbx11k/v2_fold_5.py
index 1fddcc2f..41a5ba43 100644
--- a/src/ptbench/data/tbx11k/v2_fold_5.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_5.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-5.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_6.py b/src/ptbench/config/data/tbx11k/v2_fold_6.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_6.py
rename to src/ptbench/config/data/tbx11k/v2_fold_6.py
index d9085af1..0f82163d 100644
--- a/src/ptbench/data/tbx11k/v2_fold_6.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_6.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-6.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_7.py b/src/ptbench/config/data/tbx11k/v2_fold_7.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_7.py
rename to src/ptbench/config/data/tbx11k/v2_fold_7.py
index b324e129..6f3d958b 100644
--- a/src/ptbench/data/tbx11k/v2_fold_7.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_7.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-7.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_8.py b/src/ptbench/config/data/tbx11k/v2_fold_8.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_8.py
rename to src/ptbench/config/data/tbx11k/v2_fold_8.py
index 31ed229a..3b10a652 100644
--- a/src/ptbench/data/tbx11k/v2_fold_8.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_8.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-8.json")
diff --git a/src/ptbench/data/tbx11k/v2_fold_9.py b/src/ptbench/config/data/tbx11k/v2_fold_9.py
similarity index 68%
rename from src/ptbench/data/tbx11k/v2_fold_9.py
rename to src/ptbench/config/data/tbx11k/v2_fold_9.py
index 74db9a28..86922305 100644
--- a/src/ptbench/data/tbx11k/v2_fold_9.py
+++ b/src/ptbench/config/data/tbx11k/v2_fold_9.py
@@ -6,9 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-9.json")
diff --git a/src/ptbench/data/tbx11k/v2_others_vs_atb.py b/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
similarity index 83%
rename from src/ptbench/data/tbx11k/v2_others_vs_atb.py
rename to src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
index b5f78019..a5e8c480 100644
--- a/src/ptbench/data/tbx11k/v2_others_vs_atb.py
+++ b/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
@@ -27,9 +27,10 @@ active TB cases (total samples = 8369):
- Active TB only: 157
- Total: 1793
-See :py:class:`.tbx11k.datamodule.DataModule` for technical details.
+See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+details.
"""
-from .datamodule import DataModule
+from ptbench.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-others-vs-atb.json")
diff --git a/src/ptbench/config/models/__init__.py b/src/ptbench/config/models/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/ptbench/models/config/alexnet.py b/src/ptbench/config/models/alexnet.py
similarity index 90%
rename from src/ptbench/models/config/alexnet.py
rename to src/ptbench/config/models/alexnet.py
index 9adcfec8..fce6ba64 100644
--- a/src/ptbench/models/config/alexnet.py
+++ b/src/ptbench/config/models/alexnet.py
@@ -4,7 +4,7 @@
"""AlexNet_, to be trained from scratch.
This configuration contains a version of AlexNet_ (c.f. `TorchVision's
-page <alexnet_pytorch_>`), modified for a variable number of outputs
+page <alexnet-pytorch_>`_), modified for a variable number of outputs
(defaults to 1).
"""
diff --git a/src/ptbench/models/config/alexnet_pretrained.py b/src/ptbench/config/models/alexnet_pretrained.py
similarity index 100%
rename from src/ptbench/models/config/alexnet_pretrained.py
rename to src/ptbench/config/models/alexnet_pretrained.py
diff --git a/src/ptbench/models/config/densenet.py b/src/ptbench/config/models/densenet.py
similarity index 100%
rename from src/ptbench/models/config/densenet.py
rename to src/ptbench/config/models/densenet.py
diff --git a/src/ptbench/models/config/densenet_pretrained.py b/src/ptbench/config/models/densenet_pretrained.py
similarity index 100%
rename from src/ptbench/models/config/densenet_pretrained.py
rename to src/ptbench/config/models/densenet_pretrained.py
diff --git a/src/ptbench/models/config/densenet_rs.py b/src/ptbench/config/models/densenet_rs.py
similarity index 100%
rename from src/ptbench/models/config/densenet_rs.py
rename to src/ptbench/config/models/densenet_rs.py
diff --git a/src/ptbench/models/config/logistic_regression.py b/src/ptbench/config/models/logistic_regression.py
similarity index 100%
rename from src/ptbench/models/config/logistic_regression.py
rename to src/ptbench/config/models/logistic_regression.py
diff --git a/src/ptbench/models/config/mlp.py b/src/ptbench/config/models/mlp.py
similarity index 100%
rename from src/ptbench/models/config/mlp.py
rename to src/ptbench/config/models/mlp.py
diff --git a/src/ptbench/models/config/pasa.py b/src/ptbench/config/models/pasa.py
similarity index 100%
rename from src/ptbench/models/config/pasa.py
rename to src/ptbench/config/models/pasa.py
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 888794b4..04fa19e4 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -62,8 +62,8 @@ def test_config_list():
runner = CliRunner()
result = runner.invoke(list)
_assert_exit_0(result)
- assert "module: ptbench.data" in result.output
- assert "module: ptbench.models.config" in result.output
+ assert "module: ptbench.config.data" in result.output
+ assert "module: ptbench.config.models" in result.output
@pytest.mark.skip(reason="Test need to be updated")
@@ -72,8 +72,8 @@ def test_config_list_v():
result = CliRunner().invoke(list, ["--verbose"])
_assert_exit_0(result)
- assert "module: ptbench.data" in result.output
- assert "module: ptbench.models.config" in result.output
+ assert "module: ptbench.config.data" in result.output
+ assert "module: ptbench.config.models" in result.output
def test_config_describe_help():
diff --git a/tests/test_hivtb.py b/tests/test_hivtb.py
index eb6513f0..13119812 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.data.hivtb.datamodule import make_split
+ from ptbench.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.data.hivtb"
+ f".{name}", "ptbench.config.data.hivtb"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_indian.py b/tests/test_indian.py
index de428b16..e86b56f6 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.data.indian.datamodule import make_split
+ from ptbench.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.data.indian"
+ f".{name}", "ptbench.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 973350aa..1e8227d3 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.data.montgomery.datamodule import make_split
+ from ptbench.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.data.montgomery"
+ f".{name}", "ptbench.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 4618e25f..9af425a5 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.data.montgomery"
+ f".{name}", "ptbench.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.data.shenzhen"
+ f".{name}", "ptbench.config.data.shenzhen"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.data.montgomery_shenzhen"
+ f".{name}", "ptbench.config.data.montgomery_shenzhen"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.data.montgomery"
+ ".datamodule", "ptbench.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.data.shenzhen"
+ ".datamodule", "ptbench.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 7ff4985b..b3c7f5f5 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.data.montgomery"
+ f".{name}", "ptbench.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.data.shenzhen"
+ f".{name}", "ptbench.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.data.indian"
+ f".{name}", "ptbench.config.data.indian"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.data.montgomery_shenzhen_indian"
+ f".{name}", "ptbench.config.data.montgomery_shenzhen_indian"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.data.montgomery"
+ ".datamodule", "ptbench.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.data.shenzhen"
+ ".datamodule", "ptbench.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.data.indian"
+ ".datamodule", "ptbench.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 bb1f7be4..95b59bf1 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.data.montgomery"
+ f".{name}", "ptbench.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.data.shenzhen"
+ f".{name}", "ptbench.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.data.indian"
+ f".{name}", "ptbench.config.data.indian"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.data.padchest"
+ f".{padchest_name}", "ptbench.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.data.montgomery_shenzhen_indian_padchest"
+ f".{name}", "ptbench.config.data.montgomery_shenzhen_indian_padchest"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.data.montgomery"
+ ".datamodule", "ptbench.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.data.shenzhen"
+ ".datamodule", "ptbench.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.data.indian"
+ ".datamodule", "ptbench.config.data.indian"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.data.padchest"
+ ".datamodule", "ptbench.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 6abde7b9..71956b49 100644
--- a/tests/test_montgomery_shenzhen_indian_tbx11k.py
+++ b/tests/test_montgomery_shenzhen_indian_tbx11k.py
@@ -37,39 +37,40 @@ import pytest
)
def test_split_consistency(name: str, tbx11k_name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.data.montgomery"
+ f".{name}", "ptbench.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.data.shenzhen"
+ f".{name}", "ptbench.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.data.indian"
+ f".{name}", "ptbench.config.data.indian"
).datamodule
tbx11k = importlib.import_module(
- f".{tbx11k_name}", "ptbench.data.tbx11k"
+ f".{tbx11k_name}", "ptbench.config.data.tbx11k"
).datamodule
combined = importlib.import_module(
- f".{tbx11k_name}", "ptbench.data.montgomery_shenzhen_indian_tbx11k"
+ f".{tbx11k_name}",
+ "ptbench.config.data.montgomery_shenzhen_indian_tbx11k",
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.data.montgomery"
+ ".datamodule", "ptbench.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.data.shenzhen"
+ ".datamodule", "ptbench.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.data.indian"
+ ".datamodule", "ptbench.config.data.indian"
).RawDataLoader
TBX11kLoader = importlib.import_module(
- ".datamodule", "ptbench.data.tbx11k"
+ ".datamodule", "ptbench.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 0870c99a..83f45212 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.data.nih_cxr14.datamodule import make_split
+ from ptbench.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.data.nih_cxr14"
+ f".{name}", "ptbench.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 4a9379e3..5c5bb5ef 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.data.nih_cxr14"
+ f".{name}", "ptbench.config.data.nih_cxr14"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.data.padchest"
+ f".{padchest_name}", "ptbench.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{combined_name}", "ptbench.data.nih_cxr14_padchest"
+ f".{combined_name}", "ptbench.config.data.nih_cxr14_padchest"
).datamodule
CXR14Loader = importlib.import_module(
- ".datamodule", "ptbench.data.nih_cxr14"
+ ".datamodule", "ptbench.config.data.nih_cxr14"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.data.padchest"
+ ".datamodule", "ptbench.config.data.padchest"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_padchest.py b/tests/test_padchest.py
index 4dd91623..54b42b6d 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.data.padchest.datamodule import make_split
+ from ptbench.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.data.padchest"
+ f".{name}", "ptbench.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 12532cde..b45ce0db 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.data.shenzhen.datamodule import make_split
+ from ptbench.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.data.shenzhen"
+ f".{name}", "ptbench.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 de8c55c5..0f3a7689 100644
--- a/tests/test_summary.py
+++ b/tests/test_summary.py
@@ -4,7 +4,7 @@
import unittest
-import ptbench.models.config.pasa as pasa_config
+import ptbench.config.models.pasa as pasa_config
from ptbench.utils.summary import summary
diff --git a/tests/test_tbpoc.py b/tests/test_tbpoc.py
index 7125efb1..cf3327d4 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.data.tbpoc.datamodule import make_split
+ from ptbench.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.data.tbpoc"
+ f".{name}", "ptbench.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 39c54174..0c44a85a 100644
--- a/tests/test_tbx11k.py
+++ b/tests/test_tbx11k.py
@@ -137,7 +137,7 @@ def test_protocol_consistency(
lenghts: dict[str, int],
prefixes: typing.Sequence[str],
):
- from ptbench.data.tbx11k.datamodule import make_split
+ from ptbench.config.data.tbx11k.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -187,7 +187,7 @@ def test_loading(
database_checkers, name: str, dataset: str, prefixes: typing.Sequence[str]
):
datamodule = importlib.import_module(
- f".{name}", "ptbench.data.tbx11k"
+ f".{name}", "ptbench.config.data.tbx11k"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
--
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