diff --git a/.reuse/dep5 b/.reuse/dep5
index 4e2a69c2921139df15d0edbb731375714f78b61e..9ddad99c1508e91ea62e11d08860343ad177173d 100644
--- a/.reuse/dep5
+++ b/.reuse/dep5
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: ptbench
+Upstream-Name: mednet
Upstream-Contact: Andre Anjos <andre.anjos@idiap.ch>
-Source: https://gitlab.idiap.ch/biosignal/software/ptbench
+Source: https://gitlab.idiap.ch/biosignal/software/mednet
Files:
.gitmodules
@@ -15,8 +15,8 @@ Files:
doc/results/img/*.jpg
doc/results/img/*.png
doc/results/img/*/*.jpg
- src/ptbench/config/data/*/*.json
- src/ptbench/config/data/*/*.json.bz2
+ src/mednet/config/data/*/*.json
+ src/mednet/config/data/*/*.json.bz2
tests/data/*.csv
tests/data/*.json
tests/data/*.png
diff --git a/MANIFEST.in b/MANIFEST.in
index 2d400b18f88e713e6cd69dd2ad79d22aae3d5c6d..5b589c033900e970b0d7092b59bb32904266314b 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -4,4 +4,4 @@
recursive-include doc *.rst *.png
recursive-include tests *.py *.png *.csv *.json
-recursive-include src/ptbench/config/data *.json *.json.bz2
+recursive-include src/mednet/config/data *.json *.json.bz2
diff --git a/README.md b/README.md
index 810b740dfcc9a300a220d78c6a7a885c970ecd30..12c83b1393e9f9cebecf4cc80e2a0cd0b77a2993 100644
--- a/README.md
+++ b/README.md
@@ -3,10 +3,10 @@ SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idia
SPDX-License-Identifier: GPL-3.0-or-later
-->
-[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/ptbench/main/sphinx/index.html)
-[](https://gitlab.idiap.ch/biosignal/software/ptbench/commits/main)
-[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/ptbench/main/coverage/index.html)
-[](https://gitlab.idiap.ch/biosignal/software/ptbench)
+[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/mednet/main/sphinx/index.html)
+[](https://gitlab.idiap.ch/biosignal/software/mednet/commits/main)
+[](https://www.idiap.ch/software/biosignal/docs/biosignal/software/mednet/main/coverage/index.html)
+[](https://gitlab.idiap.ch/biosignal/software/mednet)
# Computer-Aided Disease Detection from Medical Data
diff --git a/doc/api.rst b/doc/api.rst
index 54457da74cf1a82fa0c28f554b6422482b61129f..49af309e192f1948c369cc85898d26f79a86b31e 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -2,17 +2,17 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.api:
+.. _mednet.api:
============
Python API
============
This section includes information for using the Python API of
-``ptbench``.
+``mednet``.
-.. _ptbench.api.data:
+.. _mednet.api.data:
Data Methods
------------
@@ -22,14 +22,14 @@ Auxiliary classes and methods to define raw dataset iterators.
.. autosummary::
:toctree: api/data
- ptbench.data.augmentations
- ptbench.data.datamodule
- ptbench.data.image_utils
- ptbench.data.split
- ptbench.data.typing
+ mednet.data.augmentations
+ mednet.data.datamodule
+ mednet.data.image_utils
+ mednet.data.split
+ mednet.data.typing
-.. _ptbench.api.models:
+.. _mednet.api.models:
Models
------
@@ -39,16 +39,16 @@ CNN and other models implemented.
.. autosummary::
:toctree: api/models
- ptbench.models.pasa
- ptbench.models.alexnet
- ptbench.models.densenet
- ptbench.models.normalizer
- ptbench.models.logistic_regression
- ptbench.models.mlp
- ptbench.models.typing
+ mednet.models.pasa
+ mednet.models.alexnet
+ mednet.models.densenet
+ mednet.models.normalizer
+ mednet.models.logistic_regression
+ mednet.models.mlp
+ mednet.models.typing
-.. _ptbench.api.engines:
+.. _mednet.api.engines:
Command engines
---------------
@@ -58,11 +58,11 @@ Functions to actuate on the data.
.. autosummary::
:toctree: api/engine
- ptbench.engine.device
- ptbench.engine.callbacks
- ptbench.engine.trainer
- ptbench.engine.predictor
- ptbench.engine.evaluator
+ mednet.engine.device
+ mednet.engine.callbacks
+ mednet.engine.trainer
+ mednet.engine.predictor
+ mednet.engine.evaluator
.. _ptbench.api.saliency:
@@ -80,7 +80,7 @@ Engines to generate and analyze saliency mapping techniques.
ptbench.engine.saliency.interpretability
-.. _ptbench.api.utils:
+.. _mednet.api.utils:
Various utilities
-----------------
@@ -90,11 +90,11 @@ Reusable auxiliary functions.
.. autosummary::
:toctree: api/utils
- ptbench.utils.checkpointer
- ptbench.utils.rc
- ptbench.utils.resources
- ptbench.utils.summary
- ptbench.utils.tensorboard
+ mednet.utils.checkpointer
+ mednet.utils.rc
+ mednet.utils.resources
+ mednet.utils.summary
+ mednet.utils.tensorboard
.. include:: links.rst
diff --git a/doc/cli.rst b/doc/cli.rst
index 950e3cdc6182d330d5bdd40586a51eae71560e8a..0d9ebcec30502364718416371d08623e7d7d26e5 100644
--- a/doc/cli.rst
+++ b/doc/cli.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.cli:
+.. _mednet.cli:
========================
Command-line Interface
@@ -12,8 +12,8 @@ This section contains an overview of command-line applications shipped with
this package.
-.. click:: ptbench.scripts.cli:cli
- :prog: ptbench
+.. click:: mednet.scripts.cli:cli
+ :prog: mednet
:nested: full
diff --git a/doc/conf.py b/doc/conf.py
index e9d570d2b1729390ce34dfd02e3b1d64eaf83ff5..1411e92d8303f385882966b713d2b95e1d0970d1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -68,7 +68,7 @@ source_suffix = ".rst"
main_doc = "index"
# General information about the project.
-project = "ptbench"
+project = "mednet"
package = distribution(project)
copyright = "%s, Idiap Research Institute" % time.strftime("%Y")
diff --git a/doc/config.rst b/doc/config.rst
index 93c4559abe5306567cbfacb4ae6cc58fdfcd3091..1d6c5af91be6671db036e03fa5e730e20524b58a 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.config:
+.. _mednet.config:
Preset Configurations
---------------------
@@ -11,7 +11,7 @@ This module contains preset configurations for baseline CNN architectures and
datamodules.
-.. _ptbench.config.models:
+.. _mednet.config.models:
Pre-configured Models
=====================
@@ -22,17 +22,17 @@ Pre-configured models you can readily use.
:toctree: api/config.models
:template: config.rst
- ptbench.config.models.alexnet
- ptbench.config.models.alexnet_pretrained
- ptbench.config.models.densenet
- ptbench.config.models.densenet_pretrained
- ptbench.config.models.densenet_rs
- ptbench.config.models.logistic_regression
- ptbench.config.models.mlp
- ptbench.config.models.pasa
+ mednet.config.models.alexnet
+ mednet.config.models.alexnet_pretrained
+ mednet.config.models.densenet
+ mednet.config.models.densenet_pretrained
+ mednet.config.models.densenet_rs
+ mednet.config.models.logistic_regression
+ mednet.config.models.mlp
+ mednet.config.models.pasa
-.. _ptbench.config.datamodules:
+.. _mednet.config.datamodules:
DataModule support
==================
@@ -45,22 +45,22 @@ functional data module that can be used in training, prediction or testing.
.. autosummary::
:toctree: api/config.datamodules
- ptbench.config.data.hivtb.datamodule
- ptbench.config.data.indian.datamodule
- ptbench.config.data.montgomery.datamodule
- ptbench.config.data.montgomery_shenzhen.datamodule
- ptbench.config.data.montgomery_shenzhen_indian.datamodule
- ptbench.config.data.montgomery_shenzhen_indian_padchest.datamodule
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.datamodule
- ptbench.config.data.nih_cxr14.datamodule
- ptbench.config.data.nih_cxr14_padchest.datamodule
- ptbench.config.data.padchest.datamodule
- ptbench.config.data.shenzhen.datamodule
- ptbench.config.data.tbpoc.datamodule
- ptbench.config.data.tbx11k.datamodule
+ mednet.config.data.hivtb.datamodule
+ mednet.config.data.indian.datamodule
+ mednet.config.data.montgomery.datamodule
+ mednet.config.data.montgomery_shenzhen.datamodule
+ mednet.config.data.montgomery_shenzhen_indian.datamodule
+ mednet.config.data.montgomery_shenzhen_indian_padchest.datamodule
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.datamodule
+ mednet.config.data.nih_cxr14.datamodule
+ mednet.config.data.nih_cxr14_padchest.datamodule
+ mednet.config.data.padchest.datamodule
+ mednet.config.data.shenzhen.datamodule
+ mednet.config.data.tbpoc.datamodule
+ mednet.config.data.tbx11k.datamodule
-.. _ptbench.config.datamodule-instances:
+.. _mednet.config.datamodule-instances:
Pre-configured DataModules
==========================
@@ -68,29 +68,29 @@ Pre-configured DataModules
DataModules provide access to preset pytorch dataloaders for training,
validating, testing and running prediction tasks. Each of the pre-configured
DataModule is based on one (or more) of the :ref:`supported base data modules
-<ptbench.config.datamodules>`.
+<mednet.config.datamodules>`.
.. autosummary::
:toctree: api/config.datamodule-instances
:template: config.rst
- ptbench.config.data.indian.default
- ptbench.config.data.montgomery.default
- ptbench.config.data.montgomery_shenzhen.default
- ptbench.config.data.montgomery_shenzhen_indian.default
- ptbench.config.data.montgomery_shenzhen_indian_padchest.default
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
- ptbench.config.data.nih_cxr14.default
- ptbench.config.data.nih_cxr14_padchest.idiap
- ptbench.config.data.padchest.idiap
- ptbench.config.data.shenzhen.default
- ptbench.config.data.tbx11k.v1_healthy_vs_atb
- ptbench.config.data.tbx11k.v2_others_vs_atb
- ptbench.config.data.tbx11k.v2_others_vs_atb
+ mednet.config.data.indian.default
+ mednet.config.data.montgomery.default
+ mednet.config.data.montgomery_shenzhen.default
+ mednet.config.data.montgomery_shenzhen_indian.default
+ mednet.config.data.montgomery_shenzhen_indian_padchest.default
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
+ mednet.config.data.nih_cxr14.default
+ mednet.config.data.nih_cxr14_padchest.idiap
+ mednet.config.data.padchest.idiap
+ mednet.config.data.shenzhen.default
+ mednet.config.data.tbx11k.v1_healthy_vs_atb
+ mednet.config.data.tbx11k.v2_others_vs_atb
+ mednet.config.data.tbx11k.v2_others_vs_atb
-.. _ptbench.config.datamodule-instances.folds:
+.. _mednet.config.datamodule-instances.folds:
Cross-validation DataModules
============================
@@ -105,17 +105,17 @@ datamodules. Nine other folds are available for every configuration (from 1 to
:toctree: api/config.datamodule-folds
:template: config.rst
- ptbench.config.data.hivtb.fold_0
- ptbench.config.data.indian.fold_0
- ptbench.config.data.montgomery.fold_0
- ptbench.config.data.montgomery_shenzhen.fold_0
- ptbench.config.data.montgomery_shenzhen_indian.fold_0
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
- ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
- ptbench.config.data.shenzhen.fold_0
- ptbench.config.data.tbpoc.fold_0
- ptbench.config.data.tbx11k.v1_fold_0
- ptbench.config.data.tbx11k.v2_fold_0
+ mednet.config.data.hivtb.fold_0
+ mednet.config.data.indian.fold_0
+ mednet.config.data.montgomery.fold_0
+ mednet.config.data.montgomery_shenzhen.fold_0
+ mednet.config.data.montgomery_shenzhen_indian.fold_0
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
+ mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
+ mednet.config.data.shenzhen.fold_0
+ mednet.config.data.tbpoc.fold_0
+ mednet.config.data.tbx11k.v1_fold_0
+ mednet.config.data.tbx11k.v2_fold_0
.. include:: links.rst
diff --git a/doc/index.rst b/doc/index.rst
index e948754e9e4351b23f3ab668b93f9c46790cd400..b0126ac0b4051d09395d31a4eb25a88424f8a832 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench:
+.. _mednet:
====================================================
Computer-Aided Disease Detection from Medical Data
@@ -38,7 +38,7 @@ Please use the BibTeX reference below to cite this work:
number = {Idiap-Com-01-2021},
year = {2021},
institution = {Idiap},
- url = {https://gitlab.idiap.ch/biosignal/software/ptbench},
+ url = {https://gitlab.idiap.ch/biosignal/software/mednet},
pdf = {https://publidiap.idiap.ch/downloads/reports/2021/Raposo_Idiap-Com-01-2021.pdf}
}
diff --git a/doc/install.rst b/doc/install.rst
index e07e4e4587a7d36a2b9685f8d30eb2d3e89a6006..151bfef284149a33451542f16b5579f8bf487eb5 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.install:
+.. _mednet.install:
==============
Installation
@@ -17,13 +17,13 @@ We support two installation modes, through pip_, or mamba_ (conda).
.. code:: sh
- pip install ptbench
+ pip install mednet
Latest beta, from GitLab package registry:
.. code:: sh
- pip install --pre --index-url https://gitlab.idiap.ch/api/v4/groups/software/-/packages/pypi/simple --extra-index-url https://pypi.org/simple ptbench
+ pip install --pre --index-url https://gitlab.idiap.ch/api/v4/groups/software/-/packages/pypi/simple --extra-index-url https://pypi.org/simple mednet
.. tip::
@@ -37,13 +37,13 @@ We support two installation modes, through pip_, or mamba_ (conda).
.. code:: sh
- mamba install -c https://www.idiap.ch/software/biosignal/conda -c conda-forge ptbench
+ mamba install -c https://www.idiap.ch/software/biosignal/conda -c conda-forge mednet
Latest beta:
.. code:: sh
- mamba install -c https://www.idiap.ch/software/biosignal/conda/label/beta -c conda-forge ptbench
+ mamba install -c https://www.idiap.ch/software/biosignal/conda/label/beta -c conda-forge mednet
.. tip::
@@ -58,7 +58,7 @@ We support two installation modes, through pip_, or mamba_ (conda).
$ CONDA_OVERRIDE_CUDA=11.2 mamba install 'pytorch-gpu=*=cuda112*'
-.. _ptbench.setup:
+.. _mednet.setup:
Setup
-----
@@ -66,7 +66,7 @@ Setup
A configuration file may be useful to setup global options that should be often
reused. The location of the configuration file depends on the value of the
environment variable ``$XDG_CONFIG_HOME``, but defaults to
-``~/.config/ptbench.toml``. You may edit this file using your preferred
+``~/.config/mednet.toml``. You may edit this file using your preferred
editor.
Here is an example configuration file that may be useful as a starting point:
@@ -90,7 +90,7 @@ Here is an example configuration file that may be useful as a starting point:
.. code:: sh
- ptbench dataset list
+ mednet dataset list
You must procure and download datasets by yourself. The raw data is not
@@ -101,10 +101,10 @@ Here is an example configuration file that may be useful as a starting point:
.. code:: sh
- ptbench dataset check montgomery
+ mednet dataset check montgomery
-.. _ptbench.setup.databases:
+.. _mednet.setup.databases:
Supported Databases
===================
@@ -115,7 +115,7 @@ raw data can be downloaded. The list of images in each split is available
in the source code.
-.. _ptbench.setup.databases.tb:
+.. _mednet.setup.databases.tb:
Tuberculosis databases
~~~~~~~~~~~~~~~~~~~~~~
@@ -156,7 +156,7 @@ In addition to the splits presented in the following table, 10 folds
- 52
-.. _ptbench.setup.datasets.tb+signs:
+.. _mednet.setup.datasets.tb+signs:
Tuberculosis multilabel databases
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -192,7 +192,7 @@ In addition to the splits presented in the following table, 10 folds
- 2800
-.. _ptbench.setup.datasets.tbmultilabel+signs:
+.. _mednet.setup.datasets.tbmultilabel+signs:
Tuberculosis + radiological findings dataset
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -216,7 +216,7 @@ and radiological findings.
- 0
-.. _ptbench.setup.datasets.signs:
+.. _mednet.setup.datasets.signs:
Radiological findings datasets
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -247,7 +247,7 @@ information about tuberculosis.
- 4'054
-.. _ptbench.setup.datasets.hiv-tb:
+.. _mednet.setup.datasets.hiv-tb:
HIV-Tuberculosis datasets
~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/results/index.rst b/doc/results/index.rst
index 0585e912d2b2841b437312c76417d92fad4a7394..1fec86c3f6e384c816ed8805532bc2669530b06e 100644
--- a/doc/results/index.rst
+++ b/doc/results/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results:
+.. _mednet.results:
=========
Results
@@ -59,9 +59,9 @@ Stratified k-folding has been used (10 folds) to generate these results.
.. tip::
To generate the following results, you first need to predict TB on each
- fold, then use the :ref:`aggregpred command <ptbench.cli>` to aggregate the
+ fold, then use the :ref:`aggregpred command <mednet.cli>` to aggregate the
predictions together, and finally evaluate this new file using the
- :ref:`compare command <ptbench.cli>`.
+ :ref:`compare command <mednet.cli>`.
Pasa and DenseNet-121 (random initialization)
"""""""""""""""""""""""""""""""""""""""""""""
@@ -113,37 +113,37 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC
- .. figure:: img/compare_pasa_mc_ch_kfold_500.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC-CH
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH
- .. figure:: img/compare_pasa_mc_ch_in_kfold_500.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for Pasa model trained on normalized-kfold MC-CH-IN
- :py:mod:`Pasa <ptbench.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH-IN
+ :py:mod:`Pasa <mednet.config.models.pasa>`: Pasa trained on normalized-kfold MC-CH-IN
* - .. figure:: img/compare_densenet_mc_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC
- .. figure:: img/compare_densenet_mc_ch_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH
- .. figure:: img/compare_densenet_mc_ch_in_kfold_2000.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN
DenseNet-121 (pretrained on ImageNet)
"""""""""""""""""""""""""""""""""""""
@@ -180,19 +180,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC
- .. figure:: img/compare_densenetpreIN_mc_ch_kfold_600.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH
- .. figure:: img/compare_densenetpreIN_mc_ch_ch_kfold_600.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN
- :py:mod:`DenseNet <ptbench.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH-IN
+ :py:mod:`DenseNet <mednet.config.models.densenet>` DenseNet trained on normalized-kfold MC-CH-IN
Logistic Regression Classifier
""""""""""""""""""""""""""""""
@@ -229,19 +229,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC
- .. figure:: img/compare_logreg_mc_ch_kfold_100.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC-CH
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH
- .. figure:: img/compare_logreg_mc_ch_in_kfold_100.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for LogReg model trained on normalized-kfold MC-CH-IN
- :py:mod:`LogReg <ptbench.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH-IN
+ :py:mod:`LogReg <mednet.config.models.logistic_regression>`: LogReg trained on normalized-kfold MC-CH-IN
DenseNet-121 (pretrained on ImageNet and NIH CXR14)
"""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -278,19 +278,19 @@ Thresholds used:
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC (pretrained on NIH)
- .. figure:: img/compare_densenetpre_mc_ch_kfold_300.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH (pretrained on NIH)
- .. figure:: img/compare_densenetpre_mc_ch_in_kfold_300.jpg
:align: center
:scale: 50%
:alt: Testing sets ROC curves for DenseNet model trained on normalized-kfold MC-CH-IN (pretrained on NIH)
- :py:mod:`DenseNet <ptbench.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN (pretrained on NIH)
+ :py:mod:`DenseNet <mednet.config.models.densenet>`: DenseNet trained on normalized-kfold MC-CH-IN (pretrained on NIH)
Global sensitivity analysis (relevance)
@@ -301,7 +301,7 @@ Model used to generate the following figures: LogReg trained on MC-CH-IN fold 0
.. tip::
Use the ``--relevance-analysis`` argument of the :ref:`predict command
- <ptbench.cli>` to generate the following plots.
+ <mednet.cli>` to generate the following plots.
* Green color: likely TB
* Orange color: Could be TB
diff --git a/doc/results/optimization/densenet.rst b/doc/results/optimization/densenet.rst
index d6a4c1a87898e9992760d306be76dc9d860c1673..49bc27fe3f97d155d50e32b07ae1ac676212c59c 100644
--- a/doc/results/optimization/densenet.rst
+++ b/doc/results/optimization/densenet.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.densenet:
+.. _mednet.results.optimization.densenet:
=============================
Densenet model optimization
diff --git a/doc/results/optimization/logreg.rst b/doc/results/optimization/logreg.rst
index cc8f8574bddbfdeb32eb14ad4ced8e3d457789a6..e988a5247e610d4d584f21dde415b5465e04dd1c 100644
--- a/doc/results/optimization/logreg.rst
+++ b/doc/results/optimization/logreg.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.logreg:
+.. _mednet.results.optimization.logreg:
===========================
LogReg model optimization
diff --git a/doc/results/optimization/pasa.rst b/doc/results/optimization/pasa.rst
index 901d99f63cb84eecca18b8ab687600b24b97979d..5c86dc8867ced2c016424f245e2f9f2094564454 100644
--- a/doc/results/optimization/pasa.rst
+++ b/doc/results/optimization/pasa.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.pasa:
+.. _mednet.results.optimization.pasa:
=========================
Pasa model optimization
diff --git a/doc/results/optimization/signstotb.rst b/doc/results/optimization/signstotb.rst
index a7b100341ad2089743a66de37d713945ec5544a0..52f06a17c06007681b5783faa754a728c2859d45 100644
--- a/doc/results/optimization/signstotb.rst
+++ b/doc/results/optimization/signstotb.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.optimization.signstotb:
+.. _mednet.results.optimization.signstotb:
==============================
SignsToTB model optimization
diff --git a/doc/results/runtime.rst b/doc/results/runtime.rst
index 7f079c959bfe068ea5f6e896f5876fa04fd46ff0..5f1737b5a5d8ed6823ec1bfcd5f83e0a21a71120 100644
--- a/doc/results/runtime.rst
+++ b/doc/results/runtime.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.results.runtime:
+.. _mednet.results.runtime:
==============================================
Models training runtime and memory footprint
diff --git a/doc/usage/aggregpred.rst b/doc/usage/aggregpred.rst
index bcec1eef503e8017e0e242bf9695b4296e9c402c..661750bdfcdd541231833745cf99888c167c5247 100644
--- a/doc/usage/aggregpred.rst
+++ b/doc/usage/aggregpred.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.aggregpred:
+.. _mednet.usage.aggregpred:
=======================================================
Aggregate multiple prediction files into a single one
@@ -13,12 +13,12 @@ one. It can be used when doing cross-validation to aggregate the predictions of
k different models before evaluating the aggregated predictions. We input
multiple prediction files (CSV files) and output a single one.
-Use the sub-command :ref:`aggregpred <ptbench.cli>` aggregate your prediction
+Use the sub-command :ref:`aggregpred <mednet.cli>` aggregate your prediction
files together:
.. code:: sh
- ptbench aggregpred -vv path/to/fold0/predictions.csv path/to/fold1/predictions.csv --output-folder=aggregpred
+ mednet aggregpred -vv path/to/fold0/predictions.csv path/to/fold1/predictions.csv --output-folder=aggregpred
.. include:: ../links.rst
diff --git a/doc/usage/evaluation.rst b/doc/usage/evaluation.rst
index 1778e126ce2de28c1cfe123178c0c85176f61b24..d490f991c105990d81f4d29237ac2fbc49cac941 100644
--- a/doc/usage/evaluation.rst
+++ b/doc/usage/evaluation.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.evaluation:
+.. _mednet.usage.evaluation:
==========================
Inference and Evaluation
@@ -20,22 +20,22 @@ Inference
In inference (or prediction) mode, we input data, the trained model, and output
a CSV file containing the prediction outputs for every input image.
-To run inference, use the sub-command :ref:`predict <ptbench.cli>` to run
+To run inference, use the sub-command :ref:`predict <mednet.cli>` to run
prediction on an existing dataset:
.. code:: sh
- ptbench predict -vv <model> -w <path/to/model.pth> <dataset>
+ mednet predict -vv <model> -w <path/to/model.pth> <dataset>
Replace ``<model>`` and ``<dataset>`` by the appropriate :ref:`configuration
-files <ptbench.config>`. Replace ``<path/to/model.pth>`` to a path leading to
+files <mednet.config>`. Replace ``<path/to/model.pth>`` to a path leading to
the pre-trained model.
.. tip::
An option to generate grad-CAMs is available for the :py:mod:`DensenetRS
- <ptbench.config.models.densenet_rs>` model. To activate it, use the
+ <mednet.config.models.densenet_rs>` model. To activate it, use the
``--grad-cams`` argument.
.. tip::
@@ -49,29 +49,29 @@ Evaluation
In evaluation, we input a dataset and predictions to generate performance
summaries that help analysis of a trained model. Evaluation is done using the
-:ref:`evaluate command <ptbench.cli>` followed by the model and the annotated
+:ref:`evaluate command <mednet.cli>` followed by the model and the annotated
dataset configuration, and the path to the pretrained weights via the
``--weight`` argument.
-Use ``ptbench evaluate --help`` for more information.
+Use ``mednet evaluate --help`` for more information.
E.g. run evaluation on predictions from the Montgomery set, do the following:
.. code:: sh
- ptbench evaluate -vv montgomery -p /predictions/folder -o /eval/results/folder
+ mednet evaluate -vv montgomery -p /predictions/folder -o /eval/results/folder
Comparing Systems
-----------------
To compare multiple systems together and generate combined plots and tables,
-use the :ref:`compare command <ptbench.cli>`. Use ``--help`` for a quick
+use the :ref:`compare command <mednet.cli>`. Use ``--help`` for a quick
guide.
.. code:: sh
- ptbench compare -vv A A/metrics.csv B B/metrics.csv --output-figure=plot.pdf --output-table=table.txt --threshold=0.5
+ mednet compare -vv A A/metrics.csv B B/metrics.csv --output-figure=plot.pdf --output-table=table.txt --threshold=0.5
.. include:: ../links.rst
diff --git a/doc/usage/index.rst b/doc/usage/index.rst
index 34316bab8bea2d08637b90a7dd6895b2d94da10a..05dd69181eb1aca0dd8b538b844ea3efd9367870 100644
--- a/doc/usage/index.rst
+++ b/doc/usage/index.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage:
+.. _mednet.usage:
=======
Usage
@@ -14,7 +14,7 @@ tuberculosis detection with support for the following activities.
.. figure:: img/direct_vs_indirect.png
-.. _ptbench.usage.direct-detection:
+.. _mednet.usage.direct-detection:
Direct detection
----------------
@@ -31,7 +31,7 @@ Direct detection
systems.
-.. _ptbench.usage.indirect-detection:
+.. _mednet.usage.indirect-detection:
Indirect detection
------------------
@@ -52,7 +52,7 @@ Indirect detection
* Comparison: Use predictions results to compare performance of multiple
systems.
-We provide :ref:`command-line interfaces (CLI) <ptbench.cli>` that implement
+We provide :ref:`command-line interfaces (CLI) <mednet.cli>` that implement
each of the phases above. This interface is configurable using :ref:`clapper's
extensible configuration framework <clapper.config>`. In essence, each
command-line option may be provided as a variable with the same name in a
@@ -67,14 +67,14 @@ to an application.
may require complex Python types that cannot be synthetized in a single
input parameter.
-We provide a number of :ref:`preset configuration files <ptbench.config>` that
+We provide a number of :ref:`preset configuration files <mednet.config>` that
can be used in one or more of the activities described in this section. Our
command-line framework allows you to refer to these preset configuration files
using special names (a.k.a. "resources"), that procure and load these for you
automatically.
-.. _ptbench.usage.commands:
+.. _mednet.usage.commands:
Commands
--------
diff --git a/doc/usage/predtojson.rst b/doc/usage/predtojson.rst
index 81e31d2fa8422f52e739146ccf8aa951469f6806..30ff645a379f29b09d4898c12899c286929314fe 100644
--- a/doc/usage/predtojson.rst
+++ b/doc/usage/predtojson.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.predtojson:
+.. _mednet.usage.predtojson:
========================================
Converting predictions to JSON dataset
@@ -13,12 +13,12 @@ into a JSON dataset. It can be used to create new versions of TB datasets with
the predicted radiological signs to be able to use a shallow model. We input
predictions (CSV files) and output a ``dataset.json`` file.
-Use the sub-command :ref:`predtojson <ptbench.cli>` to create your JSON dataset
+Use the sub-command :ref:`predtojson <mednet.cli>` to create your JSON dataset
file:
.. code:: sh
- ptbench predtojson -vv train train/predictions.csv test test/predictions.csv --output-folder=pred_to_json
+ mednet predtojson -vv train train/predictions.csv test test/predictions.csv --output-folder=pred_to_json
.. include:: ../links.rst
diff --git a/doc/usage/training.rst b/doc/usage/training.rst
index 5eb974cc9a0e0723f9e9e72ba4c183b0c582daf2..4172732e030e6bdb5b7a9e345d2a5da75bf1022c 100644
--- a/doc/usage/training.rst
+++ b/doc/usage/training.rst
@@ -2,7 +2,7 @@
..
.. SPDX-License-Identifier: GPL-3.0-or-later
-.. _ptbench.usage.training:
+.. _mednet.usage.training:
==========
Training
@@ -11,10 +11,10 @@
Convolutional Neural Network (CNN)
----------------------------------
-To train a new CNN, use the command-line interface (CLI) application ``ptbench
+To train a new CNN, use the command-line interface (CLI) application ``mednet
train``, available on your prompt. To use this CLI, you must define the input
dataset that will be used to train the CNN, as well as the type of model that
-will be trained. You may issue ``ptbench train --help`` for a help message
+will be trained. You may issue ``mednet train --help`` for a help message
containing more detailed instructions.
.. tip::
@@ -31,23 +31,23 @@ To train Pasa CNN on the Montgomery dataset:
.. code:: sh
- ptbench train -vv pasa montgomery --batch-size=4 --epochs=150
+ mednet train -vv pasa montgomery --batch-size=4 --epochs=150
To train DensenetRS CNN on the NIH CXR14 dataset:
.. code:: sh
- ptbench train -vv nih_cxr14 densenet_rs --batch-size=8 --epochs=10
+ mednet train -vv nih_cxr14 densenet_rs --batch-size=8 --epochs=10
Logistic regressor or shallow network
-------------------------------------
To train a logistic regressor or a shallow network, use the command-line
-interface (CLI) application ``ptbench train``, available on your prompt. To use
+interface (CLI) application ``mednet train``, available on your prompt. To use
this CLI, you must define the input dataset that will be used to train the
model, as well as the type of model that will be trained.
-You may issue ``ptbench train --help`` for a help message containing more
+You may issue ``mednet train --help`` for a help message containing more
detailed instructions.
Examples
@@ -58,7 +58,7 @@ Montgomery dataset:
.. code:: sh
- ptbench train -vv logistic_regression montgomery_rs --batch-size=4 --epochs=20
+ mednet train -vv logistic_regression montgomery_rs --batch-size=4 --epochs=20
To train an multi-layer perceptron (MLP) using predictions from a densenet
@@ -67,7 +67,7 @@ dataset:
.. code:: sh
- ptbench train -vv mlp shenzhen_rs --batch-size=4 --epochs=20
+ mednet train -vv mlp shenzhen_rs --batch-size=4 --epochs=20
.. include:: ../links.rst
diff --git a/pyproject.toml b/pyproject.toml
index c80e518ff767e64a8b78bb3c933c23ffc1a78580..a8b12aae164d7f03c775022628fe418d765a66be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
-name = "ptbench"
+name = "mednet"
version = "1.0.0b0"
requires-python = ">=3.10"
description = "Benchmarks for Computer-Aided Disease Detection from Medical Data."
@@ -46,10 +46,10 @@ dependencies = [
]
[project.urls]
-documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/ptbench/main/sphinx/"
-homepage = "https://pypi.org/project/ptbench"
-repository = "https://gitlab.idiap.ch/biosignal/software/ptbench"
-changelog = "https://gitlab.idiap.ch/biosignal/software/ptbench/-/releases"
+documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/mednet/main/sphinx/"
+homepage = "https://pypi.org/project/mednet"
+repository = "https://gitlab.idiap.ch/biosignal/software/mednet"
+changelog = "https://gitlab.idiap.ch/biosignal/software/mednet/-/releases"
[project.optional-dependencies]
qa = ["pre-commit"]
@@ -65,173 +65,173 @@ doc = [
test = ["pytest", "pytest-cov", "coverage"]
[project.scripts]
-ptbench = "ptbench.scripts.cli:cli"
+mednet = "mednet.scripts.cli:cli"
-[project.entry-points."ptbench.config"]
+[project.entry-points."mednet.config"]
# models
-pasa = "ptbench.config.models.pasa"
-mlp = "ptbench.config.models.mlp"
-logistic-regression = "ptbench.config.models.logistic_regression"
-alexnet = "ptbench.config.models.alexnet"
-alexnet-pretrained = "ptbench.config.models.alexnet_pretrained"
-densenet = "ptbench.config.models.densenet"
-densenet-pretrained = "ptbench.config.models.densenet_pretrained"
+pasa = "mednet.config.models.pasa"
+mlp = "mednet.config.models.mlp"
+logistic-regression = "mednet.config.models.logistic_regression"
+alexnet = "mednet.config.models.alexnet"
+alexnet-pretrained = "mednet.config.models.alexnet_pretrained"
+densenet = "mednet.config.models.densenet"
+densenet-pretrained = "mednet.config.models.densenet_pretrained"
# montgomery dataset (and cross-validation folds)
-montgomery = "ptbench.config.data.montgomery.default"
-montgomery-f0 = "ptbench.config.data.montgomery.fold_0"
-montgomery-f1 = "ptbench.config.data.montgomery.fold_1"
-montgomery-f2 = "ptbench.config.data.montgomery.fold_2"
-montgomery-f3 = "ptbench.config.data.montgomery.fold_3"
-montgomery-f4 = "ptbench.config.data.montgomery.fold_4"
-montgomery-f5 = "ptbench.config.data.montgomery.fold_5"
-montgomery-f6 = "ptbench.config.data.montgomery.fold_6"
-montgomery-f7 = "ptbench.config.data.montgomery.fold_7"
-montgomery-f8 = "ptbench.config.data.montgomery.fold_8"
-montgomery-f9 = "ptbench.config.data.montgomery.fold_9"
+montgomery = "mednet.config.data.montgomery.default"
+montgomery-f0 = "mednet.config.data.montgomery.fold_0"
+montgomery-f1 = "mednet.config.data.montgomery.fold_1"
+montgomery-f2 = "mednet.config.data.montgomery.fold_2"
+montgomery-f3 = "mednet.config.data.montgomery.fold_3"
+montgomery-f4 = "mednet.config.data.montgomery.fold_4"
+montgomery-f5 = "mednet.config.data.montgomery.fold_5"
+montgomery-f6 = "mednet.config.data.montgomery.fold_6"
+montgomery-f7 = "mednet.config.data.montgomery.fold_7"
+montgomery-f8 = "mednet.config.data.montgomery.fold_8"
+montgomery-f9 = "mednet.config.data.montgomery.fold_9"
# shenzhen dataset (and cross-validation folds)
-shenzhen = "ptbench.config.data.shenzhen.default"
-shenzhen-f0 = "ptbench.config.data.shenzhen.fold_0"
-shenzhen-f1 = "ptbench.config.data.shenzhen.fold_1"
-shenzhen-f2 = "ptbench.config.data.shenzhen.fold_2"
-shenzhen-f3 = "ptbench.config.data.shenzhen.fold_3"
-shenzhen-f4 = "ptbench.config.data.shenzhen.fold_4"
-shenzhen-f5 = "ptbench.config.data.shenzhen.fold_5"
-shenzhen-f6 = "ptbench.config.data.shenzhen.fold_6"
-shenzhen-f7 = "ptbench.config.data.shenzhen.fold_7"
-shenzhen-f8 = "ptbench.config.data.shenzhen.fold_8"
-shenzhen-f9 = "ptbench.config.data.shenzhen.fold_9"
+shenzhen = "mednet.config.data.shenzhen.default"
+shenzhen-f0 = "mednet.config.data.shenzhen.fold_0"
+shenzhen-f1 = "mednet.config.data.shenzhen.fold_1"
+shenzhen-f2 = "mednet.config.data.shenzhen.fold_2"
+shenzhen-f3 = "mednet.config.data.shenzhen.fold_3"
+shenzhen-f4 = "mednet.config.data.shenzhen.fold_4"
+shenzhen-f5 = "mednet.config.data.shenzhen.fold_5"
+shenzhen-f6 = "mednet.config.data.shenzhen.fold_6"
+shenzhen-f7 = "mednet.config.data.shenzhen.fold_7"
+shenzhen-f8 = "mednet.config.data.shenzhen.fold_8"
+shenzhen-f9 = "mednet.config.data.shenzhen.fold_9"
# indian dataset (and cross-validation folds)
-indian = "ptbench.config.data.indian.default"
-indian-f0 = "ptbench.config.data.indian.fold_0"
-indian-f1 = "ptbench.config.data.indian.fold_1"
-indian-f2 = "ptbench.config.data.indian.fold_2"
-indian-f3 = "ptbench.config.data.indian.fold_3"
-indian-f4 = "ptbench.config.data.indian.fold_4"
-indian-f5 = "ptbench.config.data.indian.fold_5"
-indian-f6 = "ptbench.config.data.indian.fold_6"
-indian-f7 = "ptbench.config.data.indian.fold_7"
-indian-f8 = "ptbench.config.data.indian.fold_8"
-indian-f9 = "ptbench.config.data.indian.fold_9"
+indian = "mednet.config.data.indian.default"
+indian-f0 = "mednet.config.data.indian.fold_0"
+indian-f1 = "mednet.config.data.indian.fold_1"
+indian-f2 = "mednet.config.data.indian.fold_2"
+indian-f3 = "mednet.config.data.indian.fold_3"
+indian-f4 = "mednet.config.data.indian.fold_4"
+indian-f5 = "mednet.config.data.indian.fold_5"
+indian-f6 = "mednet.config.data.indian.fold_6"
+indian-f7 = "mednet.config.data.indian.fold_7"
+indian-f8 = "mednet.config.data.indian.fold_8"
+indian-f9 = "mednet.config.data.indian.fold_9"
# TBX11K dataset split 1: healthy vs active tb, and cross-validation folds
-tbx11k-v1-healthy-vs-atb = "ptbench.config.data.tbx11k.v1_healthy_vs_atb"
-tbx11k-v1-f0 = "ptbench.config.data.tbx11k.v1_fold_0"
-tbx11k-v1-f1 = "ptbench.config.data.tbx11k.v1_fold_1"
-tbx11k-v1-f2 = "ptbench.config.data.tbx11k.v1_fold_2"
-tbx11k-v1-f3 = "ptbench.config.data.tbx11k.v1_fold_3"
-tbx11k-v1-f4 = "ptbench.config.data.tbx11k.v1_fold_4"
-tbx11k-v1-f5 = "ptbench.config.data.tbx11k.v1_fold_5"
-tbx11k-v1-f6 = "ptbench.config.data.tbx11k.v1_fold_6"
-tbx11k-v1-f7 = "ptbench.config.data.tbx11k.v1_fold_7"
-tbx11k-v1-f8 = "ptbench.config.data.tbx11k.v1_fold_8"
-tbx11k-v1-f9 = "ptbench.config.data.tbx11k.v1_fold_9"
+tbx11k-v1-healthy-vs-atb = "mednet.config.data.tbx11k.v1_healthy_vs_atb"
+tbx11k-v1-f0 = "mednet.config.data.tbx11k.v1_fold_0"
+tbx11k-v1-f1 = "mednet.config.data.tbx11k.v1_fold_1"
+tbx11k-v1-f2 = "mednet.config.data.tbx11k.v1_fold_2"
+tbx11k-v1-f3 = "mednet.config.data.tbx11k.v1_fold_3"
+tbx11k-v1-f4 = "mednet.config.data.tbx11k.v1_fold_4"
+tbx11k-v1-f5 = "mednet.config.data.tbx11k.v1_fold_5"
+tbx11k-v1-f6 = "mednet.config.data.tbx11k.v1_fold_6"
+tbx11k-v1-f7 = "mednet.config.data.tbx11k.v1_fold_7"
+tbx11k-v1-f8 = "mednet.config.data.tbx11k.v1_fold_8"
+tbx11k-v1-f9 = "mednet.config.data.tbx11k.v1_fold_9"
# TBX11K dataset split 2: others vs active tb, and cross-validation folds
-tbx11k-v2-others-vs-atb = "ptbench.config.data.tbx11k.v2_others_vs_atb"
-tbx11k-v2-f0 = "ptbench.config.data.tbx11k.v2_fold_0"
-tbx11k-v2-f1 = "ptbench.config.data.tbx11k.v2_fold_1"
-tbx11k-v2-f2 = "ptbench.config.data.tbx11k.v2_fold_2"
-tbx11k-v2-f3 = "ptbench.config.data.tbx11k.v2_fold_3"
-tbx11k-v2-f4 = "ptbench.config.data.tbx11k.v2_fold_4"
-tbx11k-v2-f5 = "ptbench.config.data.tbx11k.v2_fold_5"
-tbx11k-v2-f6 = "ptbench.config.data.tbx11k.v2_fold_6"
-tbx11k-v2-f7 = "ptbench.config.data.tbx11k.v2_fold_7"
-tbx11k-v2-f8 = "ptbench.config.data.tbx11k.v2_fold_8"
-tbx11k-v2-f9 = "ptbench.config.data.tbx11k.v2_fold_9"
+tbx11k-v2-others-vs-atb = "mednet.config.data.tbx11k.v2_others_vs_atb"
+tbx11k-v2-f0 = "mednet.config.data.tbx11k.v2_fold_0"
+tbx11k-v2-f1 = "mednet.config.data.tbx11k.v2_fold_1"
+tbx11k-v2-f2 = "mednet.config.data.tbx11k.v2_fold_2"
+tbx11k-v2-f3 = "mednet.config.data.tbx11k.v2_fold_3"
+tbx11k-v2-f4 = "mednet.config.data.tbx11k.v2_fold_4"
+tbx11k-v2-f5 = "mednet.config.data.tbx11k.v2_fold_5"
+tbx11k-v2-f6 = "mednet.config.data.tbx11k.v2_fold_6"
+tbx11k-v2-f7 = "mednet.config.data.tbx11k.v2_fold_7"
+tbx11k-v2-f8 = "mednet.config.data.tbx11k.v2_fold_8"
+tbx11k-v2-f9 = "mednet.config.data.tbx11k.v2_fold_9"
# montgomery-shenzhen aggregated dataset
-montgomery-shenzhen = "ptbench.config.data.montgomery_shenzhen.default"
-montgomery-shenzhen-f0 = "ptbench.config.data.montgomery_shenzhen.fold_0"
-montgomery-shenzhen-f1 = "ptbench.config.data.montgomery_shenzhen.fold_1"
-montgomery-shenzhen-f2 = "ptbench.config.data.montgomery_shenzhen.fold_2"
-montgomery-shenzhen-f3 = "ptbench.config.data.montgomery_shenzhen.fold_3"
-montgomery-shenzhen-f4 = "ptbench.config.data.montgomery_shenzhen.fold_4"
-montgomery-shenzhen-f5 = "ptbench.config.data.montgomery_shenzhen.fold_5"
-montgomery-shenzhen-f6 = "ptbench.config.data.montgomery_shenzhen.fold_6"
-montgomery-shenzhen-f7 = "ptbench.config.data.montgomery_shenzhen.fold_7"
-montgomery-shenzhen-f8 = "ptbench.config.data.montgomery_shenzhen.fold_8"
-montgomery-shenzhen-f9 = "ptbench.config.data.montgomery_shenzhen.fold_9"
+montgomery-shenzhen = "mednet.config.data.montgomery_shenzhen.default"
+montgomery-shenzhen-f0 = "mednet.config.data.montgomery_shenzhen.fold_0"
+montgomery-shenzhen-f1 = "mednet.config.data.montgomery_shenzhen.fold_1"
+montgomery-shenzhen-f2 = "mednet.config.data.montgomery_shenzhen.fold_2"
+montgomery-shenzhen-f3 = "mednet.config.data.montgomery_shenzhen.fold_3"
+montgomery-shenzhen-f4 = "mednet.config.data.montgomery_shenzhen.fold_4"
+montgomery-shenzhen-f5 = "mednet.config.data.montgomery_shenzhen.fold_5"
+montgomery-shenzhen-f6 = "mednet.config.data.montgomery_shenzhen.fold_6"
+montgomery-shenzhen-f7 = "mednet.config.data.montgomery_shenzhen.fold_7"
+montgomery-shenzhen-f8 = "mednet.config.data.montgomery_shenzhen.fold_8"
+montgomery-shenzhen-f9 = "mednet.config.data.montgomery_shenzhen.fold_9"
# montgomery-shenzhen-indian aggregated dataset
-montgomery-shenzhen-indian = "ptbench.config.data.montgomery_shenzhen_indian.default"
-montgomery-shenzhen-indian-f0 = "ptbench.config.data.montgomery_shenzhen_indian.fold_0"
-montgomery-shenzhen-indian-f1 = "ptbench.config.data.montgomery_shenzhen_indian.fold_1"
-montgomery-shenzhen-indian-f2 = "ptbench.config.data.montgomery_shenzhen_indian.fold_2"
-montgomery-shenzhen-indian-f3 = "ptbench.config.data.montgomery_shenzhen_indian.fold_3"
-montgomery-shenzhen-indian-f4 = "ptbench.config.data.montgomery_shenzhen_indian.fold_4"
-montgomery-shenzhen-indian-f5 = "ptbench.config.data.montgomery_shenzhen_indian.fold_5"
-montgomery-shenzhen-indian-f6 = "ptbench.config.data.montgomery_shenzhen_indian.fold_6"
-montgomery-shenzhen-indian-f7 = "ptbench.config.data.montgomery_shenzhen_indian.fold_7"
-montgomery-shenzhen-indian-f8 = "ptbench.config.data.montgomery_shenzhen_indian.fold_8"
-montgomery-shenzhen-indian-f9 = "ptbench.config.data.montgomery_shenzhen_indian.fold_9"
+montgomery-shenzhen-indian = "mednet.config.data.montgomery_shenzhen_indian.default"
+montgomery-shenzhen-indian-f0 = "mednet.config.data.montgomery_shenzhen_indian.fold_0"
+montgomery-shenzhen-indian-f1 = "mednet.config.data.montgomery_shenzhen_indian.fold_1"
+montgomery-shenzhen-indian-f2 = "mednet.config.data.montgomery_shenzhen_indian.fold_2"
+montgomery-shenzhen-indian-f3 = "mednet.config.data.montgomery_shenzhen_indian.fold_3"
+montgomery-shenzhen-indian-f4 = "mednet.config.data.montgomery_shenzhen_indian.fold_4"
+montgomery-shenzhen-indian-f5 = "mednet.config.data.montgomery_shenzhen_indian.fold_5"
+montgomery-shenzhen-indian-f6 = "mednet.config.data.montgomery_shenzhen_indian.fold_6"
+montgomery-shenzhen-indian-f7 = "mednet.config.data.montgomery_shenzhen_indian.fold_7"
+montgomery-shenzhen-indian-f8 = "mednet.config.data.montgomery_shenzhen_indian.fold_8"
+montgomery-shenzhen-indian-f9 = "mednet.config.data.montgomery_shenzhen_indian.fold_9"
# montgomery-shenzhen-indian-tbx11k aggregated dataset
-montgomery-shenzhen-indian-tbx11k-v1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v1-f0 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0"
-montgomery-shenzhen-indian-tbx11k-v1-f1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1"
-montgomery-shenzhen-indian-tbx11k-v1-f2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2"
-montgomery-shenzhen-indian-tbx11k-v1-f3 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3"
-montgomery-shenzhen-indian-tbx11k-v1-f4 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4"
-montgomery-shenzhen-indian-tbx11k-v1-f5 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5"
-montgomery-shenzhen-indian-tbx11k-v1-f6 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6"
-montgomery-shenzhen-indian-tbx11k-v1-f7 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7"
-montgomery-shenzhen-indian-tbx11k-v1-f8 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8"
-montgomery-shenzhen-indian-tbx11k-v1-f9 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9"
-montgomery-shenzhen-indian-tbx11k-v2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb"
-montgomery-shenzhen-indian-tbx11k-v2-f0 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0"
-montgomery-shenzhen-indian-tbx11k-v2-f1 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1"
-montgomery-shenzhen-indian-tbx11k-v2-f2 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2"
-montgomery-shenzhen-indian-tbx11k-v2-f3 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3"
-montgomery-shenzhen-indian-tbx11k-v2-f4 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4"
-montgomery-shenzhen-indian-tbx11k-v2-f5 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5"
-montgomery-shenzhen-indian-tbx11k-v2-f6 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6"
-montgomery-shenzhen-indian-tbx11k-v2-f7 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7"
-montgomery-shenzhen-indian-tbx11k-v2-f8 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8"
-montgomery-shenzhen-indian-tbx11k-v2-f9 = "ptbench.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9"
+montgomery-shenzhen-indian-tbx11k-v1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb"
+montgomery-shenzhen-indian-tbx11k-v1-f0 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0"
+montgomery-shenzhen-indian-tbx11k-v1-f1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1"
+montgomery-shenzhen-indian-tbx11k-v1-f2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2"
+montgomery-shenzhen-indian-tbx11k-v1-f3 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3"
+montgomery-shenzhen-indian-tbx11k-v1-f4 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4"
+montgomery-shenzhen-indian-tbx11k-v1-f5 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5"
+montgomery-shenzhen-indian-tbx11k-v1-f6 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6"
+montgomery-shenzhen-indian-tbx11k-v1-f7 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7"
+montgomery-shenzhen-indian-tbx11k-v1-f8 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8"
+montgomery-shenzhen-indian-tbx11k-v1-f9 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9"
+montgomery-shenzhen-indian-tbx11k-v2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb"
+montgomery-shenzhen-indian-tbx11k-v2-f0 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0"
+montgomery-shenzhen-indian-tbx11k-v2-f1 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1"
+montgomery-shenzhen-indian-tbx11k-v2-f2 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2"
+montgomery-shenzhen-indian-tbx11k-v2-f3 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3"
+montgomery-shenzhen-indian-tbx11k-v2-f4 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4"
+montgomery-shenzhen-indian-tbx11k-v2-f5 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5"
+montgomery-shenzhen-indian-tbx11k-v2-f6 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6"
+montgomery-shenzhen-indian-tbx11k-v2-f7 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7"
+montgomery-shenzhen-indian-tbx11k-v2-f8 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8"
+montgomery-shenzhen-indian-tbx11k-v2-f9 = "mednet.config.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9"
# tbpoc dataset (only cross-validation folds)
-tbpoc-f0 = "ptbench.config.data.tbpoc.fold_0"
-tbpoc-f1 = "ptbench.config.data.tbpoc.fold_1"
-tbpoc-f2 = "ptbench.config.data.tbpoc.fold_2"
-tbpoc-f3 = "ptbench.config.data.tbpoc.fold_3"
-tbpoc-f4 = "ptbench.config.data.tbpoc.fold_4"
-tbpoc-f5 = "ptbench.config.data.tbpoc.fold_5"
-tbpoc-f6 = "ptbench.config.data.tbpoc.fold_6"
-tbpoc-f7 = "ptbench.config.data.tbpoc.fold_7"
-tbpoc-f8 = "ptbench.config.data.tbpoc.fold_8"
-tbpoc-f9 = "ptbench.config.data.tbpoc.fold_9"
+tbpoc-f0 = "mednet.config.data.tbpoc.fold_0"
+tbpoc-f1 = "mednet.config.data.tbpoc.fold_1"
+tbpoc-f2 = "mednet.config.data.tbpoc.fold_2"
+tbpoc-f3 = "mednet.config.data.tbpoc.fold_3"
+tbpoc-f4 = "mednet.config.data.tbpoc.fold_4"
+tbpoc-f5 = "mednet.config.data.tbpoc.fold_5"
+tbpoc-f6 = "mednet.config.data.tbpoc.fold_6"
+tbpoc-f7 = "mednet.config.data.tbpoc.fold_7"
+tbpoc-f8 = "mednet.config.data.tbpoc.fold_8"
+tbpoc-f9 = "mednet.config.data.tbpoc.fold_9"
# hivtb dataset (only cross-validation folds)
-hivtb-f0 = "ptbench.config.data.hivtb.fold_0"
-hivtb-f1 = "ptbench.config.data.hivtb.fold_1"
-hivtb-f2 = "ptbench.config.data.hivtb.fold_2"
-hivtb-f3 = "ptbench.config.data.hivtb.fold_3"
-hivtb-f4 = "ptbench.config.data.hivtb.fold_4"
-hivtb-f5 = "ptbench.config.data.hivtb.fold_5"
-hivtb-f6 = "ptbench.config.data.hivtb.fold_6"
-hivtb-f7 = "ptbench.config.data.hivtb.fold_7"
-hivtb-f8 = "ptbench.config.data.hivtb.fold_8"
-hivtb-f9 = "ptbench.config.data.hivtb.fold_9"
+hivtb-f0 = "mednet.config.data.hivtb.fold_0"
+hivtb-f1 = "mednet.config.data.hivtb.fold_1"
+hivtb-f2 = "mednet.config.data.hivtb.fold_2"
+hivtb-f3 = "mednet.config.data.hivtb.fold_3"
+hivtb-f4 = "mednet.config.data.hivtb.fold_4"
+hivtb-f5 = "mednet.config.data.hivtb.fold_5"
+hivtb-f6 = "mednet.config.data.hivtb.fold_6"
+hivtb-f7 = "mednet.config.data.hivtb.fold_7"
+hivtb-f8 = "mednet.config.data.hivtb.fold_8"
+hivtb-f9 = "mednet.config.data.hivtb.fold_9"
# NIH CXR14 (relabeled), multi-class (14 labels)
-nih-cxr14 = "ptbench.config.data.nih_cxr14.default"
-nih-cxr14-cardiomegaly = "ptbench.config.data.nih_cxr14.cardiomegaly"
+nih-cxr14 = "mednet.config.data.nih_cxr14.default"
+nih-cxr14-cardiomegaly = "mednet.config.data.nih_cxr14.cardiomegaly"
# PadChest, multi-class (varied number of labels)
-padchest-idiap = "ptbench.config.data.padchest.idiap"
-padchest-tb-idiap = "ptbench.config.data.padchest.tb_idiap"
-padchest-no-tb-idiap = "ptbench.config.data.padchest.no_tb_idiap"
-padchest-cardiomegaly-idiap = "ptbench.config.data.padchest.cardiomegaly_idiap"
+padchest-idiap = "mednet.config.data.padchest.idiap"
+padchest-tb-idiap = "mednet.config.data.padchest.tb_idiap"
+padchest-no-tb-idiap = "mednet.config.data.padchest.no_tb_idiap"
+padchest-cardiomegaly-idiap = "mednet.config.data.padchest.cardiomegaly_idiap"
# NIH CXR14 / PadChest aggregated dataset
-nih-cxr14-padchest = "ptbench.config.data.nih_cxr14_padchest.idiap"
+nih-cxr14-padchest = "mednet.config.data.nih_cxr14_padchest.idiap"
# montgomery-shenzhen-indian-padchest aggregated dataset
-montgomery-shenzhen-indian-padchest = "ptbench.config.data.montgomery_shenzhen_indian_padchest.default"
+montgomery-shenzhen-indian-padchest = "mednet.config.data.montgomery_shenzhen_indian_padchest.default"
[tool.setuptools]
zip-safe = true
@@ -253,6 +253,6 @@ lines_between_types = 1
line-length = 80
[tool.pytest.ini_options]
-addopts = ["--cov=ptbench", "--cov-report=term-missing", "--import-mode=append"]
+addopts = ["--cov=mednet", "--cov-report=term-missing", "--import-mode=append"]
junit_logging = "all"
junit_log_passing_tests = false
diff --git a/src/ptbench/__init__.py b/src/mednet/__init__.py
similarity index 100%
rename from src/ptbench/__init__.py
rename to src/mednet/__init__.py
diff --git a/src/ptbench/config/__init__.py b/src/mednet/config/__init__.py
similarity index 100%
rename from src/ptbench/config/__init__.py
rename to src/mednet/config/__init__.py
diff --git a/src/ptbench/config/data/__init__.py b/src/mednet/config/data/__init__.py
similarity index 100%
rename from src/ptbench/config/data/__init__.py
rename to src/mednet/config/data/__init__.py
diff --git a/src/ptbench/config/data/hivtb/__init__.py b/src/mednet/config/data/hivtb/__init__.py
similarity index 100%
rename from src/ptbench/config/data/hivtb/__init__.py
rename to src/mednet/config/data/hivtb/__init__.py
diff --git a/src/ptbench/config/data/hivtb/datamodule.py b/src/mednet/config/data/hivtb/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/hivtb/datamodule.py
rename to src/mednet/config/data/hivtb/datamodule.py
index 653743a53d2ec8a9d942136be61e0818fff01aa0..d5bf81038eb704705fc32e599edd721d6b3d18ca 100644
--- a/src/ptbench/config/data/hivtb/datamodule.py
+++ b/src/mednet/config/data/hivtb/datamodule.py
@@ -14,13 +14,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/hivtb/fold-0.json b/src/mednet/config/data/hivtb/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-0.json
rename to src/mednet/config/data/hivtb/fold-0.json
diff --git a/src/ptbench/config/data/hivtb/fold-1.json b/src/mednet/config/data/hivtb/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-1.json
rename to src/mednet/config/data/hivtb/fold-1.json
diff --git a/src/ptbench/config/data/hivtb/fold-2.json b/src/mednet/config/data/hivtb/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-2.json
rename to src/mednet/config/data/hivtb/fold-2.json
diff --git a/src/ptbench/config/data/hivtb/fold-3.json b/src/mednet/config/data/hivtb/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-3.json
rename to src/mednet/config/data/hivtb/fold-3.json
diff --git a/src/ptbench/config/data/hivtb/fold-4.json b/src/mednet/config/data/hivtb/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-4.json
rename to src/mednet/config/data/hivtb/fold-4.json
diff --git a/src/ptbench/config/data/hivtb/fold-5.json b/src/mednet/config/data/hivtb/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-5.json
rename to src/mednet/config/data/hivtb/fold-5.json
diff --git a/src/ptbench/config/data/hivtb/fold-6.json b/src/mednet/config/data/hivtb/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-6.json
rename to src/mednet/config/data/hivtb/fold-6.json
diff --git a/src/ptbench/config/data/hivtb/fold-7.json b/src/mednet/config/data/hivtb/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-7.json
rename to src/mednet/config/data/hivtb/fold-7.json
diff --git a/src/ptbench/config/data/hivtb/fold-8.json b/src/mednet/config/data/hivtb/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-8.json
rename to src/mednet/config/data/hivtb/fold-8.json
diff --git a/src/ptbench/config/data/hivtb/fold-9.json b/src/mednet/config/data/hivtb/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/hivtb/fold-9.json
rename to src/mednet/config/data/hivtb/fold-9.json
diff --git a/src/ptbench/config/data/hivtb/fold_0.py b/src/mednet/config/data/hivtb/fold_0.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_0.py
rename to src/mednet/config/data/hivtb/fold_0.py
index 4e00590f44f585e4a68f69b56fbc43b240e95a53..fb3a4c7425901e270ab446f28b4aa38151dbd503 100644
--- a/src/ptbench/config/data/hivtb/fold_0.py
+++ b/src/mednet/config/data/hivtb/fold_0.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/hivtb/fold_1.py b/src/mednet/config/data/hivtb/fold_1.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_1.py
rename to src/mednet/config/data/hivtb/fold_1.py
index 55333dd007e5e275c051cb34a6fc74bf2fddfbb2..6501367172ccfda1b1fd981c065895cfacd67e95 100644
--- a/src/ptbench/config/data/hivtb/fold_1.py
+++ b/src/mednet/config/data/hivtb/fold_1.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/hivtb/fold_2.py b/src/mednet/config/data/hivtb/fold_2.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_2.py
rename to src/mednet/config/data/hivtb/fold_2.py
index 5c8fd9b7af6c7a64c4995fe7ba240426585b5319..0436ae41b7a9375227e21ebc959d89272e80e584 100644
--- a/src/ptbench/config/data/hivtb/fold_2.py
+++ b/src/mednet/config/data/hivtb/fold_2.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/hivtb/fold_3.py b/src/mednet/config/data/hivtb/fold_3.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_3.py
rename to src/mednet/config/data/hivtb/fold_3.py
index 5d1b308c8afa6b9bb32bbc96272bfaa1985f7c18..b657bb4784e55c32af4062dd08c401b41ee665de 100644
--- a/src/ptbench/config/data/hivtb/fold_3.py
+++ b/src/mednet/config/data/hivtb/fold_3.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/hivtb/fold_4.py b/src/mednet/config/data/hivtb/fold_4.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_4.py
rename to src/mednet/config/data/hivtb/fold_4.py
index 77c2073a2b325e3c72bf9800415200739cb0e69e..9265421823555f4c1453cae8a37403aa0d914e0f 100644
--- a/src/ptbench/config/data/hivtb/fold_4.py
+++ b/src/mednet/config/data/hivtb/fold_4.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/hivtb/fold_5.py b/src/mednet/config/data/hivtb/fold_5.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_5.py
rename to src/mednet/config/data/hivtb/fold_5.py
index e06f9dd1fb3de22d4e7d32ac33c6aa66f5707205..9cce77de6cdab41f9bbf094eb68db3e6dc4b2af1 100644
--- a/src/ptbench/config/data/hivtb/fold_5.py
+++ b/src/mednet/config/data/hivtb/fold_5.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/hivtb/fold_6.py b/src/mednet/config/data/hivtb/fold_6.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_6.py
rename to src/mednet/config/data/hivtb/fold_6.py
index 4b7db6de8847059e92386c84f5a0d7fe7937edc8..b52509a8dfad7f0b3af088f07a20697bd8e4838d 100644
--- a/src/ptbench/config/data/hivtb/fold_6.py
+++ b/src/mednet/config/data/hivtb/fold_6.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/hivtb/fold_7.py b/src/mednet/config/data/hivtb/fold_7.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_7.py
rename to src/mednet/config/data/hivtb/fold_7.py
index 3670047caa59ea9bcf9b3b9c75a06553d288503c..c2af009cf6e93c2b8e4ca24787830a35d2411ca5 100644
--- a/src/ptbench/config/data/hivtb/fold_7.py
+++ b/src/mednet/config/data/hivtb/fold_7.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/hivtb/fold_8.py b/src/mednet/config/data/hivtb/fold_8.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_8.py
rename to src/mednet/config/data/hivtb/fold_8.py
index c0900d155b0bd59e9afa95cfa7eb08268fd53b3a..b76fda84a67b0fbeb90147669526008121bf07b8 100644
--- a/src/ptbench/config/data/hivtb/fold_8.py
+++ b/src/mednet/config/data/hivtb/fold_8.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/hivtb/fold_9.py b/src/mednet/config/data/hivtb/fold_9.py
similarity index 65%
rename from src/ptbench/config/data/hivtb/fold_9.py
rename to src/mednet/config/data/hivtb/fold_9.py
index 96ceb5963cf8d1d713ae3a758f34c54b4b5825f2..c2c92410b7dc5af00dc4bd04d72e88169e1c9383 100644
--- a/src/ptbench/config/data/hivtb/fold_9.py
+++ b/src/mednet/config/data/hivtb/fold_9.py
@@ -5,9 +5,9 @@
Database reference: [HIV-TB-2019]_
-See :py:class:`ptbench.config.data.hivtb.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.hivtb.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.hivtb.datamodule import DataModule
+from mednet.config.data.hivtb.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/indian/__init__.py b/src/mednet/config/data/indian/__init__.py
similarity index 100%
rename from src/ptbench/config/data/indian/__init__.py
rename to src/mednet/config/data/indian/__init__.py
diff --git a/src/ptbench/config/data/indian/datamodule.py b/src/mednet/config/data/indian/datamodule.py
similarity index 90%
rename from src/ptbench/config/data/indian/datamodule.py
rename to src/mednet/config/data/indian/datamodule.py
index 1c514f47c2e5c1f90df40de9c67ccac00fbbffc5..c8b762fc069d95df01af5715050b9788ed1b3b72 100644
--- a/src/ptbench/config/data/indian/datamodule.py
+++ b/src/mednet/config/data/indian/datamodule.py
@@ -8,10 +8,10 @@ Database reference: [INDIAN-2013]_
import importlib.resources
-from ptbench.config.data.shenzhen.datamodule import RawDataLoader
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
+from ....config.data.shenzhen.datamodule import RawDataLoader
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/indian/default.json b/src/mednet/config/data/indian/default.json
similarity index 100%
rename from src/ptbench/config/data/indian/default.json
rename to src/mednet/config/data/indian/default.json
diff --git a/src/ptbench/config/data/indian/default.py b/src/mednet/config/data/indian/default.py
similarity index 65%
rename from src/ptbench/config/data/indian/default.py
rename to src/mednet/config/data/indian/default.py
index 33bcb48d4d38e9e6f72953fe221c303a030cc6a5..9c402b8e2df213dcb9087e7048b58accef9b7827 100644
--- a/src/ptbench/config/data/indian/default.py
+++ b/src/mednet/config/data/indian/default.py
@@ -5,9 +5,9 @@
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/indian/fold-0.json b/src/mednet/config/data/indian/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-0.json
rename to src/mednet/config/data/indian/fold-0.json
diff --git a/src/ptbench/config/data/indian/fold-1.json b/src/mednet/config/data/indian/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-1.json
rename to src/mednet/config/data/indian/fold-1.json
diff --git a/src/ptbench/config/data/indian/fold-2.json b/src/mednet/config/data/indian/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-2.json
rename to src/mednet/config/data/indian/fold-2.json
diff --git a/src/ptbench/config/data/indian/fold-3.json b/src/mednet/config/data/indian/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-3.json
rename to src/mednet/config/data/indian/fold-3.json
diff --git a/src/ptbench/config/data/indian/fold-4.json b/src/mednet/config/data/indian/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-4.json
rename to src/mednet/config/data/indian/fold-4.json
diff --git a/src/ptbench/config/data/indian/fold-5.json b/src/mednet/config/data/indian/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-5.json
rename to src/mednet/config/data/indian/fold-5.json
diff --git a/src/ptbench/config/data/indian/fold-6.json b/src/mednet/config/data/indian/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-6.json
rename to src/mednet/config/data/indian/fold-6.json
diff --git a/src/ptbench/config/data/indian/fold-7.json b/src/mednet/config/data/indian/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-7.json
rename to src/mednet/config/data/indian/fold-7.json
diff --git a/src/ptbench/config/data/indian/fold-8.json b/src/mednet/config/data/indian/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-8.json
rename to src/mednet/config/data/indian/fold-8.json
diff --git a/src/ptbench/config/data/indian/fold-9.json b/src/mednet/config/data/indian/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/indian/fold-9.json
rename to src/mednet/config/data/indian/fold-9.json
diff --git a/src/ptbench/config/data/indian/fold_0.py b/src/mednet/config/data/indian/fold_0.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_0.py
rename to src/mednet/config/data/indian/fold_0.py
index 6a8e6c5be3970aac334d2dd69511eba47e6ee884..2c94e91d0a58f81581ee618a8b6199428ecdee99 100644
--- a/src/ptbench/config/data/indian/fold_0.py
+++ b/src/mednet/config/data/indian/fold_0.py
@@ -6,9 +6,9 @@ fold 0).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/indian/fold_1.py b/src/mednet/config/data/indian/fold_1.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_1.py
rename to src/mednet/config/data/indian/fold_1.py
index 029b6df6bb339e51e52bc93b7c1b46ccaecbb58d..7c7548e2e954bf057ada610dd8bf0aa5b1d041ac 100644
--- a/src/ptbench/config/data/indian/fold_1.py
+++ b/src/mednet/config/data/indian/fold_1.py
@@ -6,9 +6,9 @@ fold 1).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/indian/fold_2.py b/src/mednet/config/data/indian/fold_2.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_2.py
rename to src/mednet/config/data/indian/fold_2.py
index f54f35e5ad531eb1d7531ac28fb6ab5e8019e528..b849a5183fd3fb2154b035aa85ac14130ccb559f 100644
--- a/src/ptbench/config/data/indian/fold_2.py
+++ b/src/mednet/config/data/indian/fold_2.py
@@ -6,9 +6,9 @@ fold 2).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/indian/fold_3.py b/src/mednet/config/data/indian/fold_3.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_3.py
rename to src/mednet/config/data/indian/fold_3.py
index 0c49359219da79a20531d933ad264d3c3383227f..c992855d771761544f4cc73fcf3e6d8fd1787a2b 100644
--- a/src/ptbench/config/data/indian/fold_3.py
+++ b/src/mednet/config/data/indian/fold_3.py
@@ -6,9 +6,9 @@ fold 3).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/indian/fold_4.py b/src/mednet/config/data/indian/fold_4.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_4.py
rename to src/mednet/config/data/indian/fold_4.py
index 52a7b792d1d091d81b5bad508d99fdef1f4c683f..8385f0fea7ed608e41ab2c99b4cfe99200894823 100644
--- a/src/ptbench/config/data/indian/fold_4.py
+++ b/src/mednet/config/data/indian/fold_4.py
@@ -6,9 +6,9 @@ fold 4).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/indian/fold_5.py b/src/mednet/config/data/indian/fold_5.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_5.py
rename to src/mednet/config/data/indian/fold_5.py
index 843a1e8c8b847075c3256580268ed3331b948130..7ee271dce50bc444df7a1ca16ad957d087f2d199 100644
--- a/src/ptbench/config/data/indian/fold_5.py
+++ b/src/mednet/config/data/indian/fold_5.py
@@ -6,9 +6,9 @@ fold 5).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/indian/fold_6.py b/src/mednet/config/data/indian/fold_6.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_6.py
rename to src/mednet/config/data/indian/fold_6.py
index 9970d6f6422ae9aa7950c449af8535918ff486f7..9d5c0b94a0a2c415f0f1a949977f64a7cc00efff 100644
--- a/src/ptbench/config/data/indian/fold_6.py
+++ b/src/mednet/config/data/indian/fold_6.py
@@ -6,9 +6,9 @@ fold 6).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/indian/fold_7.py b/src/mednet/config/data/indian/fold_7.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_7.py
rename to src/mednet/config/data/indian/fold_7.py
index 5bbef8dbba072a108caa80cc28455f28cd7fcd9d..912fd422aa8ba2db8cedc6e0733e5e2a3f4bf462 100644
--- a/src/ptbench/config/data/indian/fold_7.py
+++ b/src/mednet/config/data/indian/fold_7.py
@@ -6,9 +6,9 @@ fold 7).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/indian/fold_8.py b/src/mednet/config/data/indian/fold_8.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_8.py
rename to src/mednet/config/data/indian/fold_8.py
index 0416153fc061e81d02c189128b4d0b9775697bec..b01e5426772e1c3e27eb7cc46abec2686994992b 100644
--- a/src/ptbench/config/data/indian/fold_8.py
+++ b/src/mednet/config/data/indian/fold_8.py
@@ -6,9 +6,9 @@ fold 8).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/indian/fold_9.py b/src/mednet/config/data/indian/fold_9.py
similarity index 66%
rename from src/ptbench/config/data/indian/fold_9.py
rename to src/mednet/config/data/indian/fold_9.py
index 3d4df2a51a8b721d24f6be53eca1c038393ffe35..31510e329dc446440b4131f3f45d8217eb8f5443 100644
--- a/src/ptbench/config/data/indian/fold_9.py
+++ b/src/mednet/config/data/indian/fold_9.py
@@ -6,9 +6,9 @@ fold 9).
Database reference: [INDIAN-2013]_
-See :py:class:`ptbench.config.data.indian.datamodule.DataModule` for technical details.
+See :py:class:`mednet.config.data.indian.datamodule.DataModule` for technical details.
"""
-from ptbench.config.data.indian.datamodule import DataModule
+from mednet.config.data.indian.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery/__init__.py b/src/mednet/config/data/montgomery/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery/__init__.py
rename to src/mednet/config/data/montgomery/__init__.py
diff --git a/src/ptbench/config/data/montgomery/datamodule.py b/src/mednet/config/data/montgomery/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/montgomery/datamodule.py
rename to src/mednet/config/data/montgomery/datamodule.py
index 84cdbc77d3b024fa07f4fe6a9bd6a0b8c132e6e1..ec1b7c1422a0ce4bd5948c7446c14f6d50478fb2 100644
--- a/src/ptbench/config/data/montgomery/datamodule.py
+++ b/src/mednet/config/data/montgomery/datamodule.py
@@ -13,13 +13,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/montgomery/default.json b/src/mednet/config/data/montgomery/default.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/default.json
rename to src/mednet/config/data/montgomery/default.json
diff --git a/src/ptbench/config/data/montgomery/default.py b/src/mednet/config/data/montgomery/default.py
similarity index 67%
rename from src/ptbench/config/data/montgomery/default.py
rename to src/mednet/config/data/montgomery/default.py
index fa8902107f9e81e17f89a6ca72b13c260716db54..edd014e8231350bb86e1e9fe28ab48409665c10c 100644
--- a/src/ptbench/config/data/montgomery/default.py
+++ b/src/mednet/config/data/montgomery/default.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery/fold-0.json b/src/mednet/config/data/montgomery/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-0.json
rename to src/mednet/config/data/montgomery/fold-0.json
diff --git a/src/ptbench/config/data/montgomery/fold-1.json b/src/mednet/config/data/montgomery/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-1.json
rename to src/mednet/config/data/montgomery/fold-1.json
diff --git a/src/ptbench/config/data/montgomery/fold-2.json b/src/mednet/config/data/montgomery/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-2.json
rename to src/mednet/config/data/montgomery/fold-2.json
diff --git a/src/ptbench/config/data/montgomery/fold-3.json b/src/mednet/config/data/montgomery/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-3.json
rename to src/mednet/config/data/montgomery/fold-3.json
diff --git a/src/ptbench/config/data/montgomery/fold-4.json b/src/mednet/config/data/montgomery/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-4.json
rename to src/mednet/config/data/montgomery/fold-4.json
diff --git a/src/ptbench/config/data/montgomery/fold-5.json b/src/mednet/config/data/montgomery/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-5.json
rename to src/mednet/config/data/montgomery/fold-5.json
diff --git a/src/ptbench/config/data/montgomery/fold-6.json b/src/mednet/config/data/montgomery/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-6.json
rename to src/mednet/config/data/montgomery/fold-6.json
diff --git a/src/ptbench/config/data/montgomery/fold-7.json b/src/mednet/config/data/montgomery/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-7.json
rename to src/mednet/config/data/montgomery/fold-7.json
diff --git a/src/ptbench/config/data/montgomery/fold-8.json b/src/mednet/config/data/montgomery/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-8.json
rename to src/mednet/config/data/montgomery/fold-8.json
diff --git a/src/ptbench/config/data/montgomery/fold-9.json b/src/mednet/config/data/montgomery/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/montgomery/fold-9.json
rename to src/mednet/config/data/montgomery/fold-9.json
diff --git a/src/ptbench/config/data/montgomery/fold_0.py b/src/mednet/config/data/montgomery/fold_0.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_0.py
rename to src/mednet/config/data/montgomery/fold_0.py
index 2f72873e6bc8dfe374acd3c0abf0b4fa14f59346..6d62330303dc33c2d220133b8a1677ad3499afef 100644
--- a/src/ptbench/config/data/montgomery/fold_0.py
+++ b/src/mednet/config/data/montgomery/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery/fold_1.py b/src/mednet/config/data/montgomery/fold_1.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_1.py
rename to src/mednet/config/data/montgomery/fold_1.py
index e4fd9fe8b27566a21e82118fc67b76cd9a5d9431..649f625f75266727e7beec87a5d226d959ce0798 100644
--- a/src/ptbench/config/data/montgomery/fold_1.py
+++ b/src/mednet/config/data/montgomery/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery/fold_2.py b/src/mednet/config/data/montgomery/fold_2.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_2.py
rename to src/mednet/config/data/montgomery/fold_2.py
index 903154be5eda564ffc05d128d73f278d7b19b98f..28f55b902a5f675f01b69574089820bbf060eaaa 100644
--- a/src/ptbench/config/data/montgomery/fold_2.py
+++ b/src/mednet/config/data/montgomery/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery/fold_3.py b/src/mednet/config/data/montgomery/fold_3.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_3.py
rename to src/mednet/config/data/montgomery/fold_3.py
index 27d9ebddf0f773c54e159dd8210251b962fc6baf..e357f27efb0fe79bc313112a044649c4bfb11d7a 100644
--- a/src/ptbench/config/data/montgomery/fold_3.py
+++ b/src/mednet/config/data/montgomery/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery/fold_4.py b/src/mednet/config/data/montgomery/fold_4.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_4.py
rename to src/mednet/config/data/montgomery/fold_4.py
index e5379102d27f515d7af6e691f52c498c053627bf..57402c018068cf7b24f29ce61442e73067148c4c 100644
--- a/src/ptbench/config/data/montgomery/fold_4.py
+++ b/src/mednet/config/data/montgomery/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery/fold_5.py b/src/mednet/config/data/montgomery/fold_5.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_5.py
rename to src/mednet/config/data/montgomery/fold_5.py
index feb8ac45ac0d5214cf4f15aaa2feb3962e34e52e..30b172411d3f9e726ad458bc85540fabdaddff5f 100644
--- a/src/ptbench/config/data/montgomery/fold_5.py
+++ b/src/mednet/config/data/montgomery/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery/fold_6.py b/src/mednet/config/data/montgomery/fold_6.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_6.py
rename to src/mednet/config/data/montgomery/fold_6.py
index e868c72687e825c59d08acd2d1aa98f99d54be48..d8a2a8e2ff934c02a40480f0f6709425277dcbfc 100644
--- a/src/ptbench/config/data/montgomery/fold_6.py
+++ b/src/mednet/config/data/montgomery/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery/fold_7.py b/src/mednet/config/data/montgomery/fold_7.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_7.py
rename to src/mednet/config/data/montgomery/fold_7.py
index 0415dfba481bed7aa731c117a7f5ea4c6cba30d9..86d16e0c12ce0423454f4f32f69b99830f2b40b2 100644
--- a/src/ptbench/config/data/montgomery/fold_7.py
+++ b/src/mednet/config/data/montgomery/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery/fold_8.py b/src/mednet/config/data/montgomery/fold_8.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_8.py
rename to src/mednet/config/data/montgomery/fold_8.py
index d00595b0d90358d8459cd93acfe93688a9e7d56f..67a337d2fcc8b7cda4fe888f63cbe253e7f0e933 100644
--- a/src/ptbench/config/data/montgomery/fold_8.py
+++ b/src/mednet/config/data/montgomery/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery/fold_9.py b/src/mednet/config/data/montgomery/fold_9.py
similarity index 69%
rename from src/ptbench/config/data/montgomery/fold_9.py
rename to src/mednet/config/data/montgomery/fold_9.py
index c9158fd103a4038e28e98d62eabbcfd03a64b086..032cdbfef25fc2b142910b1d754417856bcebefb 100644
--- a/src/ptbench/config/data/montgomery/fold_9.py
+++ b/src/mednet/config/data/montgomery/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.montgomery.datamodule.DataModule` for
+See :py:class:`mednet.config.data.montgomery.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.montgomery.datamodule import DataModule
+from mednet.config.data.montgomery.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/__init__.py b/src/mednet/config/data/montgomery_shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen/datamodule.py b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
similarity index 96%
rename from src/ptbench/config/data/montgomery_shenzhen/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen/datamodule.py
index 0509dd5fedf79798693be0f358b6b5449d7cf753..9699f19d7fde69565d70c8767538d0136c325ff5 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
@@ -2,8 +2,7 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ptbench.data.datamodule import ConcatDataModule
-
+from ....data.datamodule import ConcatDataModule
from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
from ..montgomery.datamodule import make_split as make_montgomery_split
from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
diff --git a/src/ptbench/config/data/montgomery_shenzhen/default.py b/src/mednet/config/data/montgomery_shenzhen/default.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen/default.py
rename to src/mednet/config/data/montgomery_shenzhen/default.py
index 5a9208f42e9e220c03e6a40c6ea28e672749ae06..bc6a1f94bbe12d77e3d31b8496b9a4795c44572d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen/default.py
@@ -7,6 +7,6 @@ split).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_0.py b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_0.py
index 722876a6e370edccfb1fac1ff48dc7f51dc8c9dd..31933cf4b67964110b79115062d239c507a3ff75 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_0.py
@@ -7,6 +7,6 @@ validation fold 0).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_1.py b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_1.py
index 81ee4224eb4ad1977007a84cb7ba3a036688cc24..8f4b3705cea93c18c4d9594f05abb122079bfdf6 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_1.py
@@ -7,6 +7,6 @@ validation fold 1).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_2.py b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_2.py
index afd77ed3ce746d7341cff4c0c97620730a71bfad..5be0fa6326633c584fa8e392e42d2accd8a65d1e 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_2.py
@@ -7,6 +7,6 @@ validation fold 2).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_3.py b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_3.py
index cc1e48a5925e49b796e0619dd4738545a4dc7f1d..4c82b55d84d22e876c2cbc7229acac61f236de24 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_3.py
@@ -7,6 +7,6 @@ validation fold 3).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_4.py b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_4.py
index b20ba0e3f2780a78e5b034e1ae44dc51ed32365f..a3514eb41a74bd05831a7cf87ce327c646f1bc9f 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_4.py
@@ -7,6 +7,6 @@ validation fold 4).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_5.py b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_5.py
index a521e26f70385db5d135c682181c560187e98ce5..c81d7788bfd0cc1da7b60f14a33282969f99604d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_5.py
@@ -7,6 +7,6 @@ validation fold 5).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_6.py b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_6.py
index 44454a52dd8d3bdcd0fd08f9f3c039a7c4384efe..69e826a55a2343019c8a7b5fe1588e48a9b259cf 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_6.py
@@ -7,6 +7,6 @@ validation fold 6).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_7.py b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_7.py
index 95128328cb26e05db7e955688376146d1d384881..6212724647b60e13d28110f50f658403dac4d4dd 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_7.py
@@ -7,6 +7,6 @@ validation fold 7).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_8.py b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_8.py
index 220ce854f2e6ca24697ee373c7b1fbfa4d33aa28..e6d610983fd82e0056665fbc8a5c716063eb71fd 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_8.py
@@ -7,6 +7,6 @@ validation fold 8).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen/fold_9.py b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen/fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen/fold_9.py
index 01fc7503cea99b2d598a221f0f8d30cd7c84fd24..c59826b3cca43910fa0c53933e54090de9c31242 100644
--- a/src/ptbench/config/data/montgomery_shenzhen/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen/fold_9.py
@@ -7,6 +7,6 @@ validation fold 9).
See :py:class:`.montgomery_shenzhen.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
similarity index 70%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
index 0bbb2c3d95cdbc2c586cfcdc5157d4bd7989ad72..2001857379da827cc03c0bf7a1a21466cadc3c79 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -4,23 +4,13 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen and Indian
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/default.py b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
similarity index 81%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/default.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/default.py
index 691885b11f73f17c4b0a4e27d32992dce9767aad..d4004d4fd27066e29826024c295f939b670a0d2a 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/default.py
@@ -7,6 +7,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
index d9df2f75255861954057f61b5c8a1a8a16b0d9a1..439919667afcb8a58c7b1f39a4120eb19e177c43 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_0.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
index e95a72bdb906e9e63b40d9508a22f04304b246a0..a400b2c57126160d3c367c483aef323d96ab0b95 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_1.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
index 1532a9fbaca33096998cf80c0cf84d75361e4184..a3fd8dd0dfd29e99c3edadc8172948d27cd14684 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_2.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
index 21605168e959d2f12df6662fa71e530677a0c73a..671e10fb94b244bcc4150224ada5f8d176935885 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_3.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
index 287afbdd3d5cc2d0590125014793d8174ef22878..df22c4aac1cb48a9d284696e763b99e52134bdb4 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_4.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
index 52fd19d2c17b429a9aee72c8b2771ea9a7f899e6..e85044381e3c5154273ce119fe5197b97a1c5bf6 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_5.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
index 7232f1c3a506407a79953b66690ec03b695458d6..962d4443e7160dacfe0a9480a36ddb27276307c9 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_6.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
index 16ba67fec66b54733b6d68f81a1c3232ded67747..bf08e64f18a92555afa97492f1a1b365c0a334b5 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_7.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
index f6d0788e244eedf9ef7b25e16b2face1054b588f..dbc23e04a9f76f724fbb15e1525030208ede585a 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_8.py
@@ -8,6 +8,6 @@ See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical
details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
index b4d9073cb6031ca37e726926bb129a8866d12062..885ffc9b25478737ba3fb9521bffbf6f01f8a25a 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian/fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/fold_9.py
@@ -7,6 +7,6 @@
See :py:class:`.montgomery_shenzhen_indian.datamodule.DataModule` for technical details.
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
similarity index 70%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index 93d0193ff42f1f82a35dea1b7487e232cdad9964..8414ad94077aa995b26ad79bf141d5d2c69ee914 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -4,29 +4,15 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and PadChest
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.padchest.datamodule import (
- RawDataLoader as PadchestLoader,
-)
-from ptbench.config.data.padchest.datamodule import (
- make_split as make_padchest_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..padchest.datamodule import RawDataLoader as PadchestLoader
+from ..padchest.datamodule import make_split as make_padchest_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
similarity index 73%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
index bc5ca3d84e86d28a6c63c3a0a97231a9be5ac698..3922eac6abcbe47eb5b265306c0786e3fd6c01cd 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_padchest/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
@@ -4,6 +4,8 @@
"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and Padchest
datasets."""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_padchest.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "tb-idiap.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/__init__.py
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
similarity index 69%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index 976155748535df1b4ada98fb837dd3b37c428e47..783f7251a6cf0f9bfd384d829bf94050bb8fce46 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -4,27 +4,15 @@
"""Aggregated datamodule composed of Montgomery, Shenzhen, Indian, and TBX11k
datasets."""
-from ptbench.config.data.indian.datamodule import RawDataLoader as IndianLoader
-from ptbench.config.data.indian.datamodule import (
- make_split as make_indian_split,
-)
-from ptbench.config.data.montgomery.datamodule import (
- RawDataLoader as MontgomeryLoader,
-)
-from ptbench.config.data.montgomery.datamodule import (
- make_split as make_montgomery_split,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- RawDataLoader as ShenzhenLoader,
-)
-from ptbench.config.data.shenzhen.datamodule import (
- make_split as make_shenzhen_split,
-)
-from ptbench.config.data.tbx11k.datamodule import RawDataLoader as TBX11kLoader
-from ptbench.config.data.tbx11k.datamodule import (
- make_split as make_tbx11k_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..indian.datamodule import RawDataLoader as IndianLoader
+from ..indian.datamodule import make_split as make_indian_split
+from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
+from ..montgomery.datamodule import make_split as make_montgomery_split
+from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..shenzhen.datamodule import make_split as make_shenzhen_split
+from ..tbx11k.datamodule import RawDataLoader as TBX11kLoader
+from ..tbx11k.datamodule import make_split as make_tbx11k_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
similarity index 85%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
index 47e8c4ba27d074b728e3fceda9f5d746df135988..6d301af045a24637cf6984035b6671c9276bf97b 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_0.py
@@ -8,6 +8,6 @@ This remix dataset combines ``fold-0`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-0`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_tbx11k.datamodule import DataModule
datamodule = DataModule("fold-0.json", "v1-fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
index 4bfa76529267f355f88f89b30a2274dcfa11f52f..f3476877d017eb9b03fa0f3a99d2ac94e33e8dd9 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_1.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-1`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-1`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-1.json", "v1-fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
index 2dbbb18ee7d8eadd8dae9514a6480fa807d2b537..ba5e0e29cb261723d17ebdc1eddfe08b7f63d36b 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_2.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-2`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-2`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-2.json", "v1-fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
index 5f808c6a2c48c7f218eaf1ad3064e6f13df8d19f..1af83edf8689962b09ec4c50a75933f4ff21492e 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_3.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-3`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-3`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-3.json", "v1-fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
index dc9ff8d6d77562d47bc524906d86676d347fd6e1..0b5aa4c0bc076a6f873517747199c54196c27b7d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_4.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-4`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-4`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-4.json", "v1-fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
index 137b3c82d3449dca500757734aa7a125f738b83d..946554e3a437f64eb78c3e08e55559659dd4f566 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_5.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-5`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-5`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-5.json", "v1-fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
index 50641ffac93c33e5b5684e0c69e5914af2084a63..29ba981daddf32f9bdd54e893ccc811b8e74b0ef 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_6.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-6`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-6`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-6.json", "v1-fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
index 54f9eaa2ab26d1563363e656dcb09e4d902c0d84..a2cf115918c5a2af0492759b420e568279d329b1 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_7.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-7`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-7`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-7.json", "v1-fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
index dbccf38c136a36eb510ca85102310f3d3daa3507..bd023982b29a5003e0155b44545b999bf3fd919c 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_8.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-8`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-8`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-8.json", "v1-fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
similarity index 82%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
index cd1b5a71da7f5b81eeee06455aea2da552f8db2d..4c64d08944fdd0ee9146da1ed2c29d04fe886bd5 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_fold_9.py
@@ -8,6 +8,8 @@ This remix dataset combines ``fold-9`` from Montgomery, Shenzhen, and Indian
datasets with ``v1-fold-9`` of TBX11k (healthy vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-9.json", "v1-fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
index 4c75b15e5ca437a04d350ad79f1540c317b89323..0ff7a0b44e80940e13a72e64c6834c75809ad704 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v1_healthy_vs_atb.py
@@ -9,6 +9,8 @@ and Indian datasets with ``v1-healthy-vs-atb`` split of TBX11k (healthy vs.
active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "v1-healthy-vs-atb.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
index 6add82d017bff0f724c24bcb8fc7d402882b7b43..e71fb091a774a8abc36a5969c0d75751e854c29d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_0.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-0`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-0.json", "v2-fold-0.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
index 09ada33a72a85a4da00939abe060477442b1c00c..0e79b6ea170ea372ec15a5c38cde9a7954604ae0 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_1.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-1`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-1.json", "v2-fold-1.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
index 756fd9a334ce7ea31b8cddf35ee3138c10048f6a..02054b2807c06bbc3707a9fd4bf64fc9e216d160 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_2.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-2`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-2.json", "v2-fold-2.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
index 8b72d4f3a3c1d7fc8e2c0b01de470c4e83b42e40..89ff7a55dcba7ac62515b64f3ea11cde934ec7ba 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_3.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-3`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-3.json", "v2-fold-3.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
index 4cb6ece8a9b4fc279d6515c79a6ba29071fd53ca..0b2fd6d115b0248c043a7263becb07ab89226bcc 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_4.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-4`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-4.json", "v2-fold-4.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
index c6b8f89e19ad91b67ebd379294abc45f001984b7..dc0d77023b3954faeb8bbd85d0fbee03695d8ec7 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_5.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-5`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-5.json", "v2-fold-5.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
index 2c09367110fd28fe5d72c9e1ae324796394bc8e9..dc2b3792f561d12294ca7101281026a0e99150f2 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_6.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-6`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-6.json", "v2-fold-6.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
index 0a7c37bcd888c9002d4e5242eb556d976d8c848d..eceb342b29ea1622c8b6806763993cf6d4ec3924 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_7.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-7`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-7.json", "v2-fold-7.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
index 5cc64e15f394653c834820410d4abcbf04a738b1..e4ff80593325b9e6ae834f0d8b96383aa1ac475d 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_8.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-8`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-8.json", "v2-fold-8.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
index b8998a232ccab969dd4d7f561b1269292940ad1c..1aeee35ecb2b0e4489423725056ada7d24b5d70b 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_fold_9.py
@@ -9,6 +9,8 @@ datasets with ``v2-fold-9`` of TBX11k (healthy, sick and latent TB vs. active
TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("fold-9.json", "v2-fold-9.json")
diff --git a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
similarity index 83%
rename from src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
rename to src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
index ccbac3529f375d0335f9508d63c2a8b655a47855..82a53cbb084b00e0e8492aa095a86d6596d5cbf7 100644
--- a/src/ptbench/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/v2_others_vs_atb.py
@@ -9,6 +9,8 @@ and Indian datasets with ``v2-others-vs-atb`` of TBX11k (healthy, sick and
latent TB vs. active TB samples).
"""
-from .datamodule import DataModule
+from mednet.data.config.montgomery_shenzhen_indian_tbx11k.datamodule import (
+ DataModule,
+)
datamodule = DataModule("default.json", "v2-others-vs-atb.json")
diff --git a/src/ptbench/config/data/nih_cxr14/__init__.py b/src/mednet/config/data/nih_cxr14/__init__.py
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/__init__.py
rename to src/mednet/config/data/nih_cxr14/__init__.py
diff --git a/src/ptbench/config/data/nih_cxr14/cardiomegaly.json b/src/mednet/config/data/nih_cxr14/cardiomegaly.json
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/cardiomegaly.json
rename to src/mednet/config/data/nih_cxr14/cardiomegaly.json
diff --git a/src/ptbench/config/data/nih_cxr14/cardiomegaly.py b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
similarity index 74%
rename from src/ptbench/config/data/nih_cxr14/cardiomegaly.py
rename to src/mednet/config/data/nih_cxr14/cardiomegaly.py
index 77248a472796b70ed7987a8d90aa610261f15ffc..8be9fde0b963123a6becccdf3c850ea193826371 100644
--- a/src/ptbench/config/data/nih_cxr14/cardiomegaly.py
+++ b/src/mednet/config/data/nih_cxr14/cardiomegaly.py
@@ -8,10 +8,10 @@ Database reference: [NIH-CXR14-2017]_
This split contains cardiomegaly cases from the NIH CXR14 database.
-See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+See :py:class:`mednet.config.data.nih_cxr14.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.nih_cxr14.datamodule import DataModule
+from mednet.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("cardiomegaly.json")
diff --git a/src/ptbench/config/data/nih_cxr14/datamodule.py b/src/mednet/config/data/nih_cxr14/datamodule.py
similarity index 95%
rename from src/ptbench/config/data/nih_cxr14/datamodule.py
rename to src/mednet/config/data/nih_cxr14/datamodule.py
index 69f044eb701c58392e5b671db1853c03393ff08c..b42f1d1c815694a213e90b0e01cd7faa6f08b321 100644
--- a/src/ptbench/config/data/nih_cxr14/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14/datamodule.py
@@ -13,12 +13,12 @@ import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/nih_cxr14/default.json.bz2 b/src/mednet/config/data/nih_cxr14/default.json.bz2
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14/default.json.bz2
rename to src/mednet/config/data/nih_cxr14/default.json.bz2
diff --git a/src/ptbench/config/data/nih_cxr14/default.py b/src/mednet/config/data/nih_cxr14/default.py
similarity index 71%
rename from src/ptbench/config/data/nih_cxr14/default.py
rename to src/mednet/config/data/nih_cxr14/default.py
index 00ac5afdc1afbf953eb528865db4e0a8dba1faee..2fa797be4371e78115516c22545a9c9d457fdc97 100644
--- a/src/ptbench/config/data/nih_cxr14/default.py
+++ b/src/mednet/config/data/nih_cxr14/default.py
@@ -7,10 +7,10 @@
* Validation samples: 6350
* Test samples: 4054
-See :py:class:`ptbench.config.data.nih_cxr14.datamodule.DataModule` for
+See :py:class:`mednet.config.data.nih_cxr14.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.nih_cxr14.datamodule import DataModule
+from mednet.config.data.nih_cxr14.datamodule import DataModule
datamodule = DataModule("default.json.bz2")
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/__init__.py b/src/mednet/config/data/nih_cxr14_padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/nih_cxr14_padchest/__init__.py
rename to src/mednet/config/data/nih_cxr14_padchest/__init__.py
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
similarity index 73%
rename from src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
rename to src/mednet/config/data/nih_cxr14_padchest/datamodule.py
index cd2d8fb237541481c6fe8a6f65d33d5ff1b98836..09fd623f9d6503429bfa7856ce162b7d3c67e49e 100644
--- a/src/ptbench/config/data/nih_cxr14_padchest/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
@@ -2,19 +2,11 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-from ptbench.config.data.nih_cxr14.datamodule import (
- RawDataLoader as CXR14Loader,
-)
-from ptbench.config.data.nih_cxr14.datamodule import (
- make_split as make_cxr14_split,
-)
-from ptbench.config.data.padchest.datamodule import (
- RawDataLoader as PadchestLoader,
-)
-from ptbench.config.data.padchest.datamodule import (
- make_split as make_padchest_split,
-)
-from ptbench.data.datamodule import ConcatDataModule
+from ....data.datamodule import ConcatDataModule
+from ..nih_cxr14.datamodule import RawDataLoader as CXR14Loader
+from ..nih_cxr14.datamodule import make_split as make_cxr14_split
+from ..padchest.datamodule import RawDataLoader as PadchestLoader
+from ..padchest.datamodule import make_split as make_padchest_split
class DataModule(ConcatDataModule):
diff --git a/src/ptbench/config/data/nih_cxr14_padchest/idiap.py b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
similarity index 81%
rename from src/ptbench/config/data/nih_cxr14_padchest/idiap.py
rename to src/mednet/config/data/nih_cxr14_padchest/idiap.py
index f318b4f73e39be6606f19df357102dac972a3b55..91d74d9b670f75607fb4daa32e0bb13c069d7f10 100644
--- a/src/ptbench/config/data/nih_cxr14_padchest/idiap.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
@@ -4,6 +4,6 @@
"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized)
datasets (no-tb-idiap split)."""
-from .datamodule import DataModule
+from mednet.data.config.nih_cx14_padchest.datamodule import DataModule
datamodule = DataModule("default.json.bz2", "no-tb-idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/__init__.py b/src/mednet/config/data/padchest/__init__.py
similarity index 100%
rename from src/ptbench/config/data/padchest/__init__.py
rename to src/mednet/config/data/padchest/__init__.py
diff --git a/src/ptbench/config/data/padchest/cardiomegaly-idiap.json b/src/mednet/config/data/padchest/cardiomegaly-idiap.json
similarity index 100%
rename from src/ptbench/config/data/padchest/cardiomegaly-idiap.json
rename to src/mednet/config/data/padchest/cardiomegaly-idiap.json
diff --git a/src/ptbench/config/data/padchest/cardiomegaly_idiap.py b/src/mednet/config/data/padchest/cardiomegaly_idiap.py
similarity index 77%
rename from src/ptbench/config/data/padchest/cardiomegaly_idiap.py
rename to src/mednet/config/data/padchest/cardiomegaly_idiap.py
index a22cdc08bbc6ea398c0606d1072d317c8e3e87a5..b8a4c0d09db1b8e4c9f103ecb18283ab4e086de4 100644
--- a/src/ptbench/config/data/padchest/cardiomegaly_idiap.py
+++ b/src/mednet/config/data/padchest/cardiomegaly_idiap.py
@@ -9,10 +9,10 @@ This split contains the first 40 images with cardiomegaly, with parameters:
Label = "Normal", MethodLabel = "Physician", Projection = "PA"
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("cardiomegaly-idiap.json")
diff --git a/src/ptbench/config/data/padchest/datamodule.py b/src/mednet/config/data/padchest/datamodule.py
similarity index 96%
rename from src/ptbench/config/data/padchest/datamodule.py
rename to src/mednet/config/data/padchest/datamodule.py
index 0122a429b33215312473228ba9db21b9fc235caf..a065deceaf9676219f9afd7234a40f9d9124de0d 100644
--- a/src/ptbench/config/data/padchest/datamodule.py
+++ b/src/mednet/config/data/padchest/datamodule.py
@@ -14,13 +14,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/padchest/idiap.json.bz2 b/src/mednet/config/data/padchest/idiap.json.bz2
similarity index 100%
rename from src/ptbench/config/data/padchest/idiap.json.bz2
rename to src/mednet/config/data/padchest/idiap.json.bz2
diff --git a/src/ptbench/config/data/padchest/idiap.py b/src/mednet/config/data/padchest/idiap.py
similarity index 77%
rename from src/ptbench/config/data/padchest/idiap.py
rename to src/mednet/config/data/padchest/idiap.py
index be0f9b2f9b5b2947f60cbc4a4b5e31da75e26d15..07afe93e591036f29b4d44eafaf473830aeafe11 100644
--- a/src/ptbench/config/data/padchest/idiap.py
+++ b/src/mednet/config/data/padchest/idiap.py
@@ -6,7 +6,7 @@
Database reference: [PADCHEST-2019]_
This split contains all images in the database. Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
* Split reference: ours
@@ -15,6 +15,6 @@ details.
* Test samples: 0
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/no-tb-idiap.json.bz2 b/src/mednet/config/data/padchest/no-tb-idiap.json.bz2
similarity index 100%
rename from src/ptbench/config/data/padchest/no-tb-idiap.json.bz2
rename to src/mednet/config/data/padchest/no-tb-idiap.json.bz2
diff --git a/src/ptbench/config/data/padchest/no_tb_idiap.py b/src/mednet/config/data/padchest/no_tb_idiap.py
similarity index 83%
rename from src/ptbench/config/data/padchest/no_tb_idiap.py
rename to src/mednet/config/data/padchest/no_tb_idiap.py
index 8c2c5fc7a48502b140ee3a0c870c6cb832b72273..79f05da51612c7ea577d902fb91fd8116e8e05d4 100644
--- a/src/ptbench/config/data/padchest/no_tb_idiap.py
+++ b/src/mednet/config/data/padchest/no_tb_idiap.py
@@ -29,10 +29,10 @@ Database reference: [PADCHEST-2019]_
* edema and consolidation
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("no-tb-idiap.json.bz2")
diff --git a/src/ptbench/config/data/padchest/tb-idiap.json b/src/mednet/config/data/padchest/tb-idiap.json
similarity index 100%
rename from src/ptbench/config/data/padchest/tb-idiap.json
rename to src/mednet/config/data/padchest/tb-idiap.json
diff --git a/src/ptbench/config/data/padchest/tb_idiap.py b/src/mednet/config/data/padchest/tb_idiap.py
similarity index 80%
rename from src/ptbench/config/data/padchest/tb_idiap.py
rename to src/mednet/config/data/padchest/tb_idiap.py
index c6c4da93caadc0720279bddf74f4e44df3722e51..bf625d711eacabac007327fc5c63967ff9e54275 100644
--- a/src/ptbench/config/data/padchest/tb_idiap.py
+++ b/src/mednet/config/data/padchest/tb_idiap.py
@@ -11,10 +11,10 @@ Projection = "PA" and TB cases. Labelling matches those for active TB (binary)
classification datasets.
Read documentation of
-:py:class:`ptbench.config.data.padchest.datamodule.DataModule` for technical
+:py:class:`mednet.config.data.padchest.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.padchest.datamodule import DataModule
+from mednet.config.data.padchest.datamodule import DataModule
datamodule = DataModule("tb-idiap.json")
diff --git a/src/ptbench/config/data/shenzhen/__init__.py b/src/mednet/config/data/shenzhen/__init__.py
similarity index 100%
rename from src/ptbench/config/data/shenzhen/__init__.py
rename to src/mednet/config/data/shenzhen/__init__.py
diff --git a/src/ptbench/config/data/shenzhen/datamodule.py b/src/mednet/config/data/shenzhen/datamodule.py
similarity index 92%
rename from src/ptbench/config/data/shenzhen/datamodule.py
rename to src/mednet/config/data/shenzhen/datamodule.py
index 70c63893fd5e5133e01fc608b708c36822426332..6409179465984e94e52c29f12bfb7bcc50b09596 100644
--- a/src/ptbench/config/data/shenzhen/datamodule.py
+++ b/src/mednet/config/data/shenzhen/datamodule.py
@@ -13,13 +13,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/shenzhen/default.json b/src/mednet/config/data/shenzhen/default.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/default.json
rename to src/mednet/config/data/shenzhen/default.json
diff --git a/src/ptbench/config/data/shenzhen/default.py b/src/mednet/config/data/shenzhen/default.py
similarity index 78%
rename from src/ptbench/config/data/shenzhen/default.py
rename to src/mednet/config/data/shenzhen/default.py
index fd0dbaf1dc04074fc9c091564c15078181614fc9..e2fa24b21510b09c549aa87ab5b71c6452a5a913 100644
--- a/src/ptbench/config/data/shenzhen/default.py
+++ b/src/mednet/config/data/shenzhen/default.py
@@ -9,10 +9,10 @@ Database reference: [MONTGOMERY-SHENZHEN-2014]_
* Validation samples: 16% of TB and healthy CXR (including labels)
* Test samples: 20% of TB and healthy CXR (including labels)
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("default.json")
diff --git a/src/ptbench/config/data/shenzhen/fold-0.json b/src/mednet/config/data/shenzhen/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-0.json
rename to src/mednet/config/data/shenzhen/fold-0.json
diff --git a/src/ptbench/config/data/shenzhen/fold-1.json b/src/mednet/config/data/shenzhen/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-1.json
rename to src/mednet/config/data/shenzhen/fold-1.json
diff --git a/src/ptbench/config/data/shenzhen/fold-2.json b/src/mednet/config/data/shenzhen/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-2.json
rename to src/mednet/config/data/shenzhen/fold-2.json
diff --git a/src/ptbench/config/data/shenzhen/fold-3.json b/src/mednet/config/data/shenzhen/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-3.json
rename to src/mednet/config/data/shenzhen/fold-3.json
diff --git a/src/ptbench/config/data/shenzhen/fold-4.json b/src/mednet/config/data/shenzhen/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-4.json
rename to src/mednet/config/data/shenzhen/fold-4.json
diff --git a/src/ptbench/config/data/shenzhen/fold-5.json b/src/mednet/config/data/shenzhen/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-5.json
rename to src/mednet/config/data/shenzhen/fold-5.json
diff --git a/src/ptbench/config/data/shenzhen/fold-6.json b/src/mednet/config/data/shenzhen/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-6.json
rename to src/mednet/config/data/shenzhen/fold-6.json
diff --git a/src/ptbench/config/data/shenzhen/fold-7.json b/src/mednet/config/data/shenzhen/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-7.json
rename to src/mednet/config/data/shenzhen/fold-7.json
diff --git a/src/ptbench/config/data/shenzhen/fold-8.json b/src/mednet/config/data/shenzhen/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-8.json
rename to src/mednet/config/data/shenzhen/fold-8.json
diff --git a/src/ptbench/config/data/shenzhen/fold-9.json b/src/mednet/config/data/shenzhen/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/shenzhen/fold-9.json
rename to src/mednet/config/data/shenzhen/fold-9.json
diff --git a/src/ptbench/config/data/shenzhen/fold_0.py b/src/mednet/config/data/shenzhen/fold_0.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_0.py
rename to src/mednet/config/data/shenzhen/fold_0.py
index 890250dba8e7c9780fb9873a0203e5fd65f11de0..17ab27e504e1467da338d22a860a7a1de7fb9bc8 100644
--- a/src/ptbench/config/data/shenzhen/fold_0.py
+++ b/src/mednet/config/data/shenzhen/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_1.py b/src/mednet/config/data/shenzhen/fold_1.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_1.py
rename to src/mednet/config/data/shenzhen/fold_1.py
index ff95e0d052b7beab85e1c6196b79d9e86dba5e16..61ea13aa984be81b5f94f740c4848f374659d35f 100644
--- a/src/ptbench/config/data/shenzhen/fold_1.py
+++ b/src/mednet/config/data/shenzhen/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_2.py b/src/mednet/config/data/shenzhen/fold_2.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_2.py
rename to src/mednet/config/data/shenzhen/fold_2.py
index db16495c2b3b205ffabf4c920d3a198967d2fb34..edb9247796cb6baa1f1cea0b72ad8ac3728b1f48 100644
--- a/src/ptbench/config/data/shenzhen/fold_2.py
+++ b/src/mednet/config/data/shenzhen/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_3.py b/src/mednet/config/data/shenzhen/fold_3.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_3.py
rename to src/mednet/config/data/shenzhen/fold_3.py
index d0321c8696c168ad83d5910641699233ce7425a9..618008481b7c2892448d1dbe205cda68e33764b7 100644
--- a/src/ptbench/config/data/shenzhen/fold_3.py
+++ b/src/mednet/config/data/shenzhen/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_4.py b/src/mednet/config/data/shenzhen/fold_4.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_4.py
rename to src/mednet/config/data/shenzhen/fold_4.py
index f6760358546c2daa9712bc2c618c9dd1b118b557..478af2ee758e675722d0578a316a33f7a0e47898 100644
--- a/src/ptbench/config/data/shenzhen/fold_4.py
+++ b/src/mednet/config/data/shenzhen/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_5.py b/src/mednet/config/data/shenzhen/fold_5.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_5.py
rename to src/mednet/config/data/shenzhen/fold_5.py
index 6d77a8409a5813d6451f4346b7217c120bbee992..21dcf8ff1ec64781172cb01976e4f7eca2b79d1f 100644
--- a/src/ptbench/config/data/shenzhen/fold_5.py
+++ b/src/mednet/config/data/shenzhen/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_6.py b/src/mednet/config/data/shenzhen/fold_6.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_6.py
rename to src/mednet/config/data/shenzhen/fold_6.py
index 3ecd646ebb15ed34a2863a924497fa391e2dd881..fbc6aac8cb40ca898790040edcffda62999ae3e9 100644
--- a/src/ptbench/config/data/shenzhen/fold_6.py
+++ b/src/mednet/config/data/shenzhen/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_7.py b/src/mednet/config/data/shenzhen/fold_7.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_7.py
rename to src/mednet/config/data/shenzhen/fold_7.py
index 61ba5d27a1062f3f971282b659e9801712b139c4..204f7b0b2cc981229ba4252acd4ca0fb99983f04 100644
--- a/src/ptbench/config/data/shenzhen/fold_7.py
+++ b/src/mednet/config/data/shenzhen/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_8.py b/src/mednet/config/data/shenzhen/fold_8.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_8.py
rename to src/mednet/config/data/shenzhen/fold_8.py
index a03121d5653ebcdf719eccb7d89ddd3a8d54b4f9..3679fa18b58af7f5eba68d5e41eca06fcbfa5232 100644
--- a/src/ptbench/config/data/shenzhen/fold_8.py
+++ b/src/mednet/config/data/shenzhen/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/shenzhen/fold_9.py b/src/mednet/config/data/shenzhen/fold_9.py
similarity index 70%
rename from src/ptbench/config/data/shenzhen/fold_9.py
rename to src/mednet/config/data/shenzhen/fold_9.py
index 168031c80166bfc76de482231851248846009388..32afdbd8b786f94597198f3bf99ac38a9e6773a9 100644
--- a/src/ptbench/config/data/shenzhen/fold_9.py
+++ b/src/mednet/config/data/shenzhen/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [MONTGOMERY-SHENZHEN-2014]_
-See :py:class:`ptbench.config.data.shenzhen.datamodule.DataModule` for
+See :py:class:`mednet.config.data.shenzhen.datamodule.DataModule` for
technical details.
"""
-from ptbench.config.data.shenzhen.datamodule import DataModule
+from mednet.config.data.shenzhen.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/tbpoc/__init__.py b/src/mednet/config/data/tbpoc/__init__.py
similarity index 100%
rename from src/ptbench/config/data/tbpoc/__init__.py
rename to src/mednet/config/data/tbpoc/__init__.py
diff --git a/src/ptbench/config/data/tbpoc/datamodule.py b/src/mednet/config/data/tbpoc/datamodule.py
similarity index 91%
rename from src/ptbench/config/data/tbpoc/datamodule.py
rename to src/mednet/config/data/tbpoc/datamodule.py
index 42a3a10f31db87e8f37f7721c06de4751ae17d61..ffe59568fd9524962e534deac1a72fcc1408cedd 100644
--- a/src/ptbench/config/data/tbpoc/datamodule.py
+++ b/src/mednet/config/data/tbpoc/datamodule.py
@@ -9,13 +9,13 @@ import PIL.Image
from torchvision.transforms.functional import center_crop, to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.image_utils import remove_black_borders
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.image_utils import remove_black_borders
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/tbpoc/fold-0.json b/src/mednet/config/data/tbpoc/fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-0.json
rename to src/mednet/config/data/tbpoc/fold-0.json
diff --git a/src/ptbench/config/data/tbpoc/fold-1.json b/src/mednet/config/data/tbpoc/fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-1.json
rename to src/mednet/config/data/tbpoc/fold-1.json
diff --git a/src/ptbench/config/data/tbpoc/fold-2.json b/src/mednet/config/data/tbpoc/fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-2.json
rename to src/mednet/config/data/tbpoc/fold-2.json
diff --git a/src/ptbench/config/data/tbpoc/fold-3.json b/src/mednet/config/data/tbpoc/fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-3.json
rename to src/mednet/config/data/tbpoc/fold-3.json
diff --git a/src/ptbench/config/data/tbpoc/fold-4.json b/src/mednet/config/data/tbpoc/fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-4.json
rename to src/mednet/config/data/tbpoc/fold-4.json
diff --git a/src/ptbench/config/data/tbpoc/fold-5.json b/src/mednet/config/data/tbpoc/fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-5.json
rename to src/mednet/config/data/tbpoc/fold-5.json
diff --git a/src/ptbench/config/data/tbpoc/fold-6.json b/src/mednet/config/data/tbpoc/fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-6.json
rename to src/mednet/config/data/tbpoc/fold-6.json
diff --git a/src/ptbench/config/data/tbpoc/fold-7.json b/src/mednet/config/data/tbpoc/fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-7.json
rename to src/mednet/config/data/tbpoc/fold-7.json
diff --git a/src/ptbench/config/data/tbpoc/fold-8.json b/src/mednet/config/data/tbpoc/fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-8.json
rename to src/mednet/config/data/tbpoc/fold-8.json
diff --git a/src/ptbench/config/data/tbpoc/fold-9.json b/src/mednet/config/data/tbpoc/fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbpoc/fold-9.json
rename to src/mednet/config/data/tbpoc/fold-9.json
diff --git a/src/ptbench/config/data/tbpoc/fold_0.py b/src/mednet/config/data/tbpoc/fold_0.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_0.py
rename to src/mednet/config/data/tbpoc/fold_0.py
index e3a0d24221d1ba3b95d3d2015adf1e0dca53d194..03b5f6cdd2b5d2a2e3ad9fb3f28cd18e2cc889a9 100644
--- a/src/ptbench/config/data/tbpoc/fold_0.py
+++ b/src/mednet/config/data/tbpoc/fold_0.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-0.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_1.py b/src/mednet/config/data/tbpoc/fold_1.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_1.py
rename to src/mednet/config/data/tbpoc/fold_1.py
index b6a04095a2f5e76d6ff37a5622f1b1bdad37500a..5db4436748cca3612849487e714b338c7d77a6f1 100644
--- a/src/ptbench/config/data/tbpoc/fold_1.py
+++ b/src/mednet/config/data/tbpoc/fold_1.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-1.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_2.py b/src/mednet/config/data/tbpoc/fold_2.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_2.py
rename to src/mednet/config/data/tbpoc/fold_2.py
index c821f0cc0eb1d4a4085cf1b93c36cd8b751262e9..5dea9179fb4fc790216fbaa3a0d81c74afa12715 100644
--- a/src/ptbench/config/data/tbpoc/fold_2.py
+++ b/src/mednet/config/data/tbpoc/fold_2.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-2.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_3.py b/src/mednet/config/data/tbpoc/fold_3.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_3.py
rename to src/mednet/config/data/tbpoc/fold_3.py
index c5c9fa7daf28e5a2e84ab85a62be5fc7dd380af2..bce854fc9c8a6a55c409bcf84dcaa0934e29b066 100644
--- a/src/ptbench/config/data/tbpoc/fold_3.py
+++ b/src/mednet/config/data/tbpoc/fold_3.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-3.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_4.py b/src/mednet/config/data/tbpoc/fold_4.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_4.py
rename to src/mednet/config/data/tbpoc/fold_4.py
index 9b3b74d9c41f307286cb5ad017f6ec1677906b1f..55720bd307bebfc7d74dfde086f1d8a881051b11 100644
--- a/src/ptbench/config/data/tbpoc/fold_4.py
+++ b/src/mednet/config/data/tbpoc/fold_4.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-4.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_5.py b/src/mednet/config/data/tbpoc/fold_5.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_5.py
rename to src/mednet/config/data/tbpoc/fold_5.py
index 7a9947dcd432cba2c1c29dcc2e611b2f173afe94..61bc52b54d9e539538ee900a077a802aa75772f5 100644
--- a/src/ptbench/config/data/tbpoc/fold_5.py
+++ b/src/mednet/config/data/tbpoc/fold_5.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-5.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_6.py b/src/mednet/config/data/tbpoc/fold_6.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_6.py
rename to src/mednet/config/data/tbpoc/fold_6.py
index 0e6a7349494077d834e18099bccf65dce83dffd2..b7f166e6b0d480bef430cb920e76f157db9cfb34 100644
--- a/src/ptbench/config/data/tbpoc/fold_6.py
+++ b/src/mednet/config/data/tbpoc/fold_6.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-6.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_7.py b/src/mednet/config/data/tbpoc/fold_7.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_7.py
rename to src/mednet/config/data/tbpoc/fold_7.py
index bb257c8efaa7a4f65ea59766716546434291a48f..3efab4a9eba71837d1eacc06c7bc41abb6855853 100644
--- a/src/ptbench/config/data/tbpoc/fold_7.py
+++ b/src/mednet/config/data/tbpoc/fold_7.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-7.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_8.py b/src/mednet/config/data/tbpoc/fold_8.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_8.py
rename to src/mednet/config/data/tbpoc/fold_8.py
index 790f13c954d7f27d9616c9e07db87a0ae9065f20..f23b85d5bf012e1a3ac1cf2506ffca9efc192ade 100644
--- a/src/ptbench/config/data/tbpoc/fold_8.py
+++ b/src/mednet/config/data/tbpoc/fold_8.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-8.json")
diff --git a/src/ptbench/config/data/tbpoc/fold_9.py b/src/mednet/config/data/tbpoc/fold_9.py
similarity index 67%
rename from src/ptbench/config/data/tbpoc/fold_9.py
rename to src/mednet/config/data/tbpoc/fold_9.py
index a53852a6aeb7a593f6b04a95c031dc6f66525988..0391b39cd5d9cfa955114cee4463d77c07c8dfdc 100644
--- a/src/ptbench/config/data/tbpoc/fold_9.py
+++ b/src/mednet/config/data/tbpoc/fold_9.py
@@ -5,10 +5,10 @@
Database reference: [TB-POC-2018]_
-See :py:class:`ptbench.config.data.tbpoc.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbpoc.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbpoc.datamodule import DataModule
+from mednet.config.data.tbpoc.datamodule import DataModule
datamodule = DataModule("fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/__init__.py b/src/mednet/config/data/tbx11k/__init__.py
similarity index 100%
rename from src/ptbench/config/data/tbx11k/__init__.py
rename to src/mednet/config/data/tbx11k/__init__.py
diff --git a/src/ptbench/config/data/tbx11k/datamodule.py b/src/mednet/config/data/tbx11k/datamodule.py
similarity index 97%
rename from src/ptbench/config/data/tbx11k/datamodule.py
rename to src/mednet/config/data/tbx11k/datamodule.py
index abe2bec7d35cf451fb98cca977fa69558935613b..ae71e46b87863b1a7134f396df5a49a2dfe0f6b0 100644
--- a/src/ptbench/config/data/tbx11k/datamodule.py
+++ b/src/mednet/config/data/tbx11k/datamodule.py
@@ -14,12 +14,12 @@ import typing_extensions
from torch.utils.data._utils.collate import default_collate_fn_map
from torchvision.transforms.functional import to_tensor
-from ptbench.data.datamodule import CachingDataModule
-from ptbench.data.split import JSONDatabaseSplit
-from ptbench.data.typing import DatabaseSplit
-from ptbench.data.typing import RawDataLoader as _BaseRawDataLoader
-from ptbench.data.typing import Sample
-from ptbench.utils.rc import load_rc
+from ....data.datamodule import CachingDataModule
+from ....data.split import JSONDatabaseSplit
+from ....data.typing import DatabaseSplit
+from ....data.typing import RawDataLoader as _BaseRawDataLoader
+from ....data.typing import Sample
+from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/ptbench/config/data/tbx11k/make_splits_from_database.py b/src/mednet/config/data/tbx11k/make_splits_from_database.py
similarity index 99%
rename from src/ptbench/config/data/tbx11k/make_splits_from_database.py
rename to src/mednet/config/data/tbx11k/make_splits_from_database.py
index 6584c25156fcdf73b45da140bc7fb46f17c1ce38..c432a2979c225a880d122a3b384cf17e3eb82194 100644
--- a/src/ptbench/config/data/tbx11k/make_splits_from_database.py
+++ b/src/mednet/config/data/tbx11k/make_splits_from_database.py
@@ -2,7 +2,7 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""Converts TBX11k JSON annotation files into simplified JSON datasets for
-ptbench.
+mednet.
Requires ``datadir.tbx11k`` to be set on your configuration file, or that you
are sitting at the root directory of the database.
@@ -362,7 +362,7 @@ def main():
from clapper.rc import UserDefaults
datadir = pathlib.Path(
- UserDefaults("ptbench.toml").get(
+ UserDefaults("mednet.toml").get(
"datadir.tbx11k", os.path.realpath(os.curdir)
)
)
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-0.json b/src/mednet/config/data/tbx11k/v1-fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-0.json
rename to src/mednet/config/data/tbx11k/v1-fold-0.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-1.json b/src/mednet/config/data/tbx11k/v1-fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-1.json
rename to src/mednet/config/data/tbx11k/v1-fold-1.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-2.json b/src/mednet/config/data/tbx11k/v1-fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-2.json
rename to src/mednet/config/data/tbx11k/v1-fold-2.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-3.json b/src/mednet/config/data/tbx11k/v1-fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-3.json
rename to src/mednet/config/data/tbx11k/v1-fold-3.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-4.json b/src/mednet/config/data/tbx11k/v1-fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-4.json
rename to src/mednet/config/data/tbx11k/v1-fold-4.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-5.json b/src/mednet/config/data/tbx11k/v1-fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-5.json
rename to src/mednet/config/data/tbx11k/v1-fold-5.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-6.json b/src/mednet/config/data/tbx11k/v1-fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-6.json
rename to src/mednet/config/data/tbx11k/v1-fold-6.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-7.json b/src/mednet/config/data/tbx11k/v1-fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-7.json
rename to src/mednet/config/data/tbx11k/v1-fold-7.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-8.json b/src/mednet/config/data/tbx11k/v1-fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-8.json
rename to src/mednet/config/data/tbx11k/v1-fold-8.json
diff --git a/src/ptbench/config/data/tbx11k/v1-fold-9.json b/src/mednet/config/data/tbx11k/v1-fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-fold-9.json
rename to src/mednet/config/data/tbx11k/v1-fold-9.json
diff --git a/src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json b/src/mednet/config/data/tbx11k/v1-healthy-vs-atb.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v1-healthy-vs-atb.json
rename to src/mednet/config/data/tbx11k/v1-healthy-vs-atb.json
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_0.py b/src/mednet/config/data/tbx11k/v1_fold_0.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_0.py
rename to src/mednet/config/data/tbx11k/v1_fold_0.py
index 9ba42d5231c0ce47de84d360e0bf753d3a0b3fde..f2d5daa5beb241fb47e2301e0f77af3e1b869f93 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_0.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_0.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-0.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_1.py b/src/mednet/config/data/tbx11k/v1_fold_1.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_1.py
rename to src/mednet/config/data/tbx11k/v1_fold_1.py
index ca3fe10400d20e2a384d1e0f505a962df3ec9ed4..f137be5962848952cb0efd72902acbe03c55b099 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_1.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_1.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-1.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_2.py b/src/mednet/config/data/tbx11k/v1_fold_2.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_2.py
rename to src/mednet/config/data/tbx11k/v1_fold_2.py
index c3ec4fe440a6a191427696bae6ef573bfb223619..cee8bcd282a4658f00b82737c1158f346da3be87 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_2.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_2.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-2.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_3.py b/src/mednet/config/data/tbx11k/v1_fold_3.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_3.py
rename to src/mednet/config/data/tbx11k/v1_fold_3.py
index 09fb16b27f600517e82c3dfee197d324b23b0080..5527c47a4b9de39ff6d992a4115ea0f113e79fed 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_3.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_3.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-3.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_4.py b/src/mednet/config/data/tbx11k/v1_fold_4.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_4.py
rename to src/mednet/config/data/tbx11k/v1_fold_4.py
index 8f96d1e540a4de75922f5c891979bbd3407b8374..800239d5866c0010f0390e26c5daa8f46f40e3ee 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_4.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_4.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-4.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_5.py b/src/mednet/config/data/tbx11k/v1_fold_5.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_5.py
rename to src/mednet/config/data/tbx11k/v1_fold_5.py
index 8ced06d43f229d85f5decb9d05b030dfc1f63a1e..e0ca7876f76baea4a204dd4a1f61eac7ba2d20b1 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_5.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_5.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-5.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_6.py b/src/mednet/config/data/tbx11k/v1_fold_6.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_6.py
rename to src/mednet/config/data/tbx11k/v1_fold_6.py
index 28e9f16a7523b45285d9d57f4c90bf61c5a98b96..79ba3cd580f6b4b44df33855ba42afe727996aca 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_6.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_6.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-6.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_7.py b/src/mednet/config/data/tbx11k/v1_fold_7.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_7.py
rename to src/mednet/config/data/tbx11k/v1_fold_7.py
index 09886b940800e5f6eb7a33e442f068b08c834822..e873f8583667c7c39643bbe32f1b67ce7c582025 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_7.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_7.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-7.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_8.py b/src/mednet/config/data/tbx11k/v1_fold_8.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_8.py
rename to src/mednet/config/data/tbx11k/v1_fold_8.py
index 5fd2dd23acbc6c3c30e397c650a7da262c1317da..21aea93e946328107de50a6911a738f4f09e6160 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_8.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_8.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-8.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_fold_9.py b/src/mednet/config/data/tbx11k/v1_fold_9.py
similarity index 69%
rename from src/ptbench/config/data/tbx11k/v1_fold_9.py
rename to src/mednet/config/data/tbx11k/v1_fold_9.py
index 440f724f694569cd76dbfa2b2ecba9c51723c322..47e0ae339b5fc47c090c13c0e0a572833724bddb 100644
--- a/src/ptbench/config/data/tbx11k/v1_fold_9.py
+++ b/src/mednet/config/data/tbx11k/v1_fold_9.py
@@ -6,10 +6,10 @@ cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py b/src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
similarity index 82%
rename from src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
rename to src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
index 785b6bfbcfe63089a2492658a632f16791c1c40f..b97d7a52fe168f0f3721f64325a32c1362460817 100644
--- a/src/ptbench/config/data/tbx11k/v1_healthy_vs_atb.py
+++ b/src/mednet/config/data/tbx11k/v1_healthy_vs_atb.py
@@ -27,10 +27,10 @@ Split v1 contains healthy subjects against active TB cases (total samples =
- Active TB only: 157
- Total: 957
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v1-healthy-vs-atb.json")
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-0.json b/src/mednet/config/data/tbx11k/v2-fold-0.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-0.json
rename to src/mednet/config/data/tbx11k/v2-fold-0.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-1.json b/src/mednet/config/data/tbx11k/v2-fold-1.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-1.json
rename to src/mednet/config/data/tbx11k/v2-fold-1.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-2.json b/src/mednet/config/data/tbx11k/v2-fold-2.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-2.json
rename to src/mednet/config/data/tbx11k/v2-fold-2.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-3.json b/src/mednet/config/data/tbx11k/v2-fold-3.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-3.json
rename to src/mednet/config/data/tbx11k/v2-fold-3.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-4.json b/src/mednet/config/data/tbx11k/v2-fold-4.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-4.json
rename to src/mednet/config/data/tbx11k/v2-fold-4.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-5.json b/src/mednet/config/data/tbx11k/v2-fold-5.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-5.json
rename to src/mednet/config/data/tbx11k/v2-fold-5.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-6.json b/src/mednet/config/data/tbx11k/v2-fold-6.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-6.json
rename to src/mednet/config/data/tbx11k/v2-fold-6.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-7.json b/src/mednet/config/data/tbx11k/v2-fold-7.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-7.json
rename to src/mednet/config/data/tbx11k/v2-fold-7.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-8.json b/src/mednet/config/data/tbx11k/v2-fold-8.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-8.json
rename to src/mednet/config/data/tbx11k/v2-fold-8.json
diff --git a/src/ptbench/config/data/tbx11k/v2-fold-9.json b/src/mednet/config/data/tbx11k/v2-fold-9.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-fold-9.json
rename to src/mednet/config/data/tbx11k/v2-fold-9.json
diff --git a/src/ptbench/config/data/tbx11k/v2-others-vs-atb.json b/src/mednet/config/data/tbx11k/v2-others-vs-atb.json
similarity index 100%
rename from src/ptbench/config/data/tbx11k/v2-others-vs-atb.json
rename to src/mednet/config/data/tbx11k/v2-others-vs-atb.json
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_0.py b/src/mednet/config/data/tbx11k/v2_fold_0.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_0.py
rename to src/mednet/config/data/tbx11k/v2_fold_0.py
index c713c4799c01dbb92e388d0e3eb49fcf635d0bdc..565bc70653cb1edfe9c5dd40d93b52106b8f5645 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_0.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_0.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-0.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_1.py b/src/mednet/config/data/tbx11k/v2_fold_1.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_1.py
rename to src/mednet/config/data/tbx11k/v2_fold_1.py
index 10b3b183366f572f1445eaa54bd213f4317189f6..77d73704df6040328b0d317dd7c8145b074a2596 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_1.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_1.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-1.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_2.py b/src/mednet/config/data/tbx11k/v2_fold_2.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_2.py
rename to src/mednet/config/data/tbx11k/v2_fold_2.py
index f7fd10a680dd849dccd9bc5d9c76475d57190eff..eac8cb9ae2c0f24c0efc97a1c0c232d133c26c6a 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_2.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_2.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-2.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_3.py b/src/mednet/config/data/tbx11k/v2_fold_3.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_3.py
rename to src/mednet/config/data/tbx11k/v2_fold_3.py
index b744251d208e72b1dd60e0b14faf9eecdcf9c7de..ec0de16516d41408db300f2970cec962dec7d5e4 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_3.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_3.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-3.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_4.py b/src/mednet/config/data/tbx11k/v2_fold_4.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_4.py
rename to src/mednet/config/data/tbx11k/v2_fold_4.py
index 17215495e6f94c2fe9013e7d9363bb1f807f51d8..f3491d51ab18672b9441b10d2b0eb94b6b4eec1f 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_4.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_4.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-4.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_5.py b/src/mednet/config/data/tbx11k/v2_fold_5.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_5.py
rename to src/mednet/config/data/tbx11k/v2_fold_5.py
index 41a5ba43aeadc4e38dc5fb77aa837f4d5874fabc..9cb818a42cbb3583fe2e4da8118fbaac923ac020 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_5.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_5.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-5.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_6.py b/src/mednet/config/data/tbx11k/v2_fold_6.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_6.py
rename to src/mednet/config/data/tbx11k/v2_fold_6.py
index 0f82163ddba31cc4bf756891ffbe7339cefb77f7..15014857119e8613ac9c585e303f72cf15236fac 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_6.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_6.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-6.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_7.py b/src/mednet/config/data/tbx11k/v2_fold_7.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_7.py
rename to src/mednet/config/data/tbx11k/v2_fold_7.py
index 6f3d958bdf32435e7ca7ec21b2b7652eb0c3c5e3..c3a63f6cf542f38a6fe4e561028dbaa6af910f29 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_7.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_7.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-7.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_8.py b/src/mednet/config/data/tbx11k/v2_fold_8.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_8.py
rename to src/mednet/config/data/tbx11k/v2_fold_8.py
index 3b10a65298d41e83aa0c0228ab88e50e563daf07..0a4f348eab015215a0fa92a4db5fa639f91bee05 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_8.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_8.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-8.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_fold_9.py b/src/mednet/config/data/tbx11k/v2_fold_9.py
similarity index 70%
rename from src/ptbench/config/data/tbx11k/v2_fold_9.py
rename to src/mednet/config/data/tbx11k/v2_fold_9.py
index 8692230521407db7e0deb204d274d023221503b0..2c087bd498fb652a219d7c477d6251ffce6c0ae8 100644
--- a/src/ptbench/config/data/tbx11k/v2_fold_9.py
+++ b/src/mednet/config/data/tbx11k/v2_fold_9.py
@@ -6,10 +6,10 @@ TB vs. active TB cases).
Database reference: [TBX11K-2020]_
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-fold-9.json")
diff --git a/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py b/src/mednet/config/data/tbx11k/v2_others_vs_atb.py
similarity index 84%
rename from src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
rename to src/mednet/config/data/tbx11k/v2_others_vs_atb.py
index a5e8c480995360bbb04b3da486047cb852b4dd37..5f50e19d290e84d8961e3ef0e66cb47a96199fc2 100644
--- a/src/ptbench/config/data/tbx11k/v2_others_vs_atb.py
+++ b/src/mednet/config/data/tbx11k/v2_others_vs_atb.py
@@ -27,10 +27,10 @@ active TB cases (total samples = 8369):
- Active TB only: 157
- Total: 1793
-See :py:class:`ptbench.config.data.tbx11k.datamodule.DataModule` for technical
+See :py:class:`mednet.config.data.tbx11k.datamodule.DataModule` for technical
details.
"""
-from ptbench.config.data.tbx11k.datamodule import DataModule
+from mednet.config.data.tbx11k.datamodule import DataModule
datamodule = DataModule("v2-others-vs-atb.json")
diff --git a/src/ptbench/config/models/__init__.py b/src/mednet/config/models/__init__.py
similarity index 100%
rename from src/ptbench/config/models/__init__.py
rename to src/mednet/config/models/__init__.py
diff --git a/src/ptbench/config/models/alexnet.py b/src/mednet/config/models/alexnet.py
similarity index 86%
rename from src/ptbench/config/models/alexnet.py
rename to src/mednet/config/models/alexnet.py
index fce6ba645f002038705c83e7674f5faebfad133f..9703f964a476b53d5aa076242bb0b02cedfe75ff 100644
--- a/src/ptbench/config/models/alexnet.py
+++ b/src/mednet/config/models/alexnet.py
@@ -11,8 +11,8 @@ page <alexnet-pytorch_>`_), modified for a variable number of outputs
from torch.nn import BCEWithLogitsLoss
from torch.optim import SGD
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.alexnet import Alexnet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.alexnet import Alexnet
model = Alexnet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/alexnet_pretrained.py b/src/mednet/config/models/alexnet_pretrained.py
similarity index 87%
rename from src/ptbench/config/models/alexnet_pretrained.py
rename to src/mednet/config/models/alexnet_pretrained.py
index 81f72b87d3fc4c67aa851dccacb74ca30476b4fb..8887db8f6f006cd2580dabac44202055a5cdacab 100644
--- a/src/ptbench/config/models/alexnet_pretrained.py
+++ b/src/mednet/config/models/alexnet_pretrained.py
@@ -13,8 +13,8 @@ N.B.: The output layer is **always** initialized from scratch.
from torch.nn import BCEWithLogitsLoss
from torch.optim import SGD
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.alexnet import Alexnet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.alexnet import Alexnet
model = Alexnet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet.py b/src/mednet/config/models/densenet.py
similarity index 86%
rename from src/ptbench/config/models/densenet.py
rename to src/mednet/config/models/densenet.py
index bfee577f97c6ba869a555b4eb50ee595c95c2c7c..9fbf388d26fab33f16ae95d19e90763aa39cdcc9 100644
--- a/src/ptbench/config/models/densenet.py
+++ b/src/mednet/config/models/densenet.py
@@ -11,8 +11,8 @@ page <densenet_pytorch_>`), modified for a variable number of outputs
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet_pretrained.py b/src/mednet/config/models/densenet_pretrained.py
similarity index 87%
rename from src/ptbench/config/models/densenet_pretrained.py
rename to src/mednet/config/models/densenet_pretrained.py
index 9b1fa4caeb18b8a6c64b99c92d554d132af0e562..7d85d9b4bc3904f887569d266fd489b31b28a171 100644
--- a/src/ptbench/config/models/densenet_pretrained.py
+++ b/src/mednet/config/models/densenet_pretrained.py
@@ -13,8 +13,8 @@ N.B.: The output layer is **always** initialized from scratch.
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/densenet_rs.py b/src/mednet/config/models/densenet_rs.py
similarity index 88%
rename from src/ptbench/config/models/densenet_rs.py
rename to src/mednet/config/models/densenet_rs.py
index 3f625686dfd8c43f5b9d65af5f6eab39d297c4ff..24caef8681a2b908782ec93cc222bc0d6ca3117b 100644
--- a/src/ptbench/config/models/densenet_rs.py
+++ b/src/mednet/config/models/densenet_rs.py
@@ -12,8 +12,8 @@ weights from scratch for radiological sign detection.
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.densenet import Densenet
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.densenet import Densenet
model = Densenet(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/config/models/logistic_regression.py b/src/mednet/config/models/logistic_regression.py
similarity index 86%
rename from src/ptbench/config/models/logistic_regression.py
rename to src/mednet/config/models/logistic_regression.py
index b93589df32e496c7352a11a92c94479a7f71ae31..bd327ed4dd5582417907471c9c352f1bb384c718 100644
--- a/src/ptbench/config/models/logistic_regression.py
+++ b/src/mednet/config/models/logistic_regression.py
@@ -8,6 +8,6 @@ the output of :py:mod:`.densenet_rs` and be trained for binary classification
(e.g. for active TB detection).
"""
-from ptbench.models.logistic_regression import LogisticRegression
+from mednet.models.logistic_regression import LogisticRegression
model = LogisticRegression(input_size=14)
diff --git a/src/ptbench/config/models/mlp.py b/src/mednet/config/models/mlp.py
similarity index 87%
rename from src/ptbench/config/models/mlp.py
rename to src/mednet/config/models/mlp.py
index c87432d77f75270f7a14430126b8be4c9a33594d..4791a8400a577808af2e70879303c69bf2893453 100644
--- a/src/ptbench/config/models/mlp.py
+++ b/src/mednet/config/models/mlp.py
@@ -8,6 +8,6 @@ output (e.g. to predict active TB presence from radiological finding
estimates).
"""
-from ptbench.models.mlp import MultiLayerPerceptron
+from mednet.models.mlp import MultiLayerPerceptron
model = MultiLayerPerceptron()
diff --git a/src/ptbench/config/models/pasa.py b/src/mednet/config/models/pasa.py
similarity index 88%
rename from src/ptbench/config/models/pasa.py
rename to src/mednet/config/models/pasa.py
index c419b5fe024859f7b2da21b67e4a7cbd3cdb927b..227b9b426568bebf327c1ac3f206a5fc3f2b44b6 100644
--- a/src/ptbench/config/models/pasa.py
+++ b/src/mednet/config/models/pasa.py
@@ -13,8 +13,8 @@ Reference: [PASA-2019]_
from torch.nn import BCEWithLogitsLoss
from torch.optim import Adam
-from ptbench.data.augmentations import ElasticDeformation
-from ptbench.models.pasa import Pasa
+from mednet.data.augmentations import ElasticDeformation
+from mednet.models.pasa import Pasa
model = Pasa(
train_loss=BCEWithLogitsLoss(),
diff --git a/src/ptbench/data/__init__.py b/src/mednet/data/__init__.py
similarity index 100%
rename from src/ptbench/data/__init__.py
rename to src/mednet/data/__init__.py
diff --git a/src/ptbench/data/augmentations.py b/src/mednet/data/augmentations.py
similarity index 100%
rename from src/ptbench/data/augmentations.py
rename to src/mednet/data/augmentations.py
diff --git a/src/ptbench/data/datamodule.py b/src/mednet/data/datamodule.py
similarity index 100%
rename from src/ptbench/data/datamodule.py
rename to src/mednet/data/datamodule.py
diff --git a/src/ptbench/data/image_utils.py b/src/mednet/data/image_utils.py
similarity index 100%
rename from src/ptbench/data/image_utils.py
rename to src/mednet/data/image_utils.py
diff --git a/src/ptbench/data/split.py b/src/mednet/data/split.py
similarity index 100%
rename from src/ptbench/data/split.py
rename to src/mednet/data/split.py
diff --git a/src/ptbench/data/typing.py b/src/mednet/data/typing.py
similarity index 100%
rename from src/ptbench/data/typing.py
rename to src/mednet/data/typing.py
diff --git a/src/ptbench/engine/__init__.py b/src/mednet/engine/__init__.py
similarity index 100%
rename from src/ptbench/engine/__init__.py
rename to src/mednet/engine/__init__.py
diff --git a/src/ptbench/engine/callbacks.py b/src/mednet/engine/callbacks.py
similarity index 100%
rename from src/ptbench/engine/callbacks.py
rename to src/mednet/engine/callbacks.py
diff --git a/src/ptbench/engine/device.py b/src/mednet/engine/device.py
similarity index 100%
rename from src/ptbench/engine/device.py
rename to src/mednet/engine/device.py
diff --git a/src/ptbench/engine/evaluator.py b/src/mednet/engine/evaluator.py
similarity index 100%
rename from src/ptbench/engine/evaluator.py
rename to src/mednet/engine/evaluator.py
diff --git a/src/ptbench/engine/loggers.py b/src/mednet/engine/loggers.py
similarity index 100%
rename from src/ptbench/engine/loggers.py
rename to src/mednet/engine/loggers.py
diff --git a/src/ptbench/engine/predictor.py b/src/mednet/engine/predictor.py
similarity index 100%
rename from src/ptbench/engine/predictor.py
rename to src/mednet/engine/predictor.py
diff --git a/src/ptbench/engine/trainer.py b/src/mednet/engine/trainer.py
similarity index 100%
rename from src/ptbench/engine/trainer.py
rename to src/mednet/engine/trainer.py
diff --git a/src/ptbench/models/__init__.py b/src/mednet/models/__init__.py
similarity index 100%
rename from src/ptbench/models/__init__.py
rename to src/mednet/models/__init__.py
diff --git a/src/ptbench/models/alexnet.py b/src/mednet/models/alexnet.py
similarity index 100%
rename from src/ptbench/models/alexnet.py
rename to src/mednet/models/alexnet.py
diff --git a/src/ptbench/models/densenet.py b/src/mednet/models/densenet.py
similarity index 100%
rename from src/ptbench/models/densenet.py
rename to src/mednet/models/densenet.py
diff --git a/src/ptbench/models/logistic_regression.py b/src/mednet/models/logistic_regression.py
similarity index 100%
rename from src/ptbench/models/logistic_regression.py
rename to src/mednet/models/logistic_regression.py
diff --git a/src/ptbench/models/loss_weights.py b/src/mednet/models/loss_weights.py
similarity index 100%
rename from src/ptbench/models/loss_weights.py
rename to src/mednet/models/loss_weights.py
diff --git a/src/ptbench/models/mlp.py b/src/mednet/models/mlp.py
similarity index 100%
rename from src/ptbench/models/mlp.py
rename to src/mednet/models/mlp.py
diff --git a/src/ptbench/models/normalizer.py b/src/mednet/models/normalizer.py
similarity index 100%
rename from src/ptbench/models/normalizer.py
rename to src/mednet/models/normalizer.py
diff --git a/src/ptbench/models/pasa.py b/src/mednet/models/pasa.py
similarity index 100%
rename from src/ptbench/models/pasa.py
rename to src/mednet/models/pasa.py
diff --git a/src/ptbench/models/separate.py b/src/mednet/models/separate.py
similarity index 100%
rename from src/ptbench/models/separate.py
rename to src/mednet/models/separate.py
diff --git a/src/ptbench/models/transforms.py b/src/mednet/models/transforms.py
similarity index 100%
rename from src/ptbench/models/transforms.py
rename to src/mednet/models/transforms.py
diff --git a/src/ptbench/models/typing.py b/src/mednet/models/typing.py
similarity index 100%
rename from src/ptbench/models/typing.py
rename to src/mednet/models/typing.py
diff --git a/src/ptbench/scripts/__init__.py b/src/mednet/scripts/__init__.py
similarity index 100%
rename from src/ptbench/scripts/__init__.py
rename to src/mednet/scripts/__init__.py
diff --git a/src/ptbench/scripts/cli.py b/src/mednet/scripts/cli.py
similarity index 100%
rename from src/ptbench/scripts/cli.py
rename to src/mednet/scripts/cli.py
diff --git a/src/ptbench/scripts/click.py b/src/mednet/scripts/click.py
similarity index 100%
rename from src/ptbench/scripts/click.py
rename to src/mednet/scripts/click.py
diff --git a/src/ptbench/scripts/config.py b/src/mednet/scripts/config.py
similarity index 92%
rename from src/ptbench/scripts/config.py
rename to src/mednet/scripts/config.py
index d8c105c5b62eea3983ddcc830fd0ec3af6d75c09..14abfe9aef185dd47e25cf22542731da72fb66fc 100644
--- a/src/ptbench/scripts/config.py
+++ b/src/mednet/scripts/config.py
@@ -24,11 +24,11 @@ def config():
epilog="""Examples:
\b
- 1. Lists all configuration resources (type: ptbench.config) installed:
+ 1. Lists all configuration resources (type: mednet.config) installed:
.. code:: sh
- ptbench config list
+ mednet config list
\b
@@ -37,7 +37,7 @@ def config():
.. code:: sh
- ptbench config list -v
+ mednet config list -v
"""
)
@@ -45,7 +45,7 @@ def config():
def list(verbose) -> None:
"""Lists configuration files installed."""
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
@@ -102,7 +102,7 @@ def list(verbose) -> None:
.. code:: sh
- ptbench config describe montgomery
+ mednet config describe montgomery
\b
@@ -111,7 +111,7 @@ def list(verbose) -> None:
.. code:: sh
- ptbench config describe montgomery -v
+ mednet config describe montgomery -v
"""
)
@@ -124,7 +124,7 @@ def list(verbose) -> None:
def describe(name, verbose) -> None:
"""Describes a specific configuration file."""
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
@@ -157,7 +157,7 @@ def describe(name, verbose) -> None:
.. code:: sh
- $ ptbench config copy montgomery -vvv newdataset.py
+ $ mednet config copy montgomery -vvv newdataset.py
"""
)
@@ -177,7 +177,7 @@ def copy(source, destination) -> None:
import shutil
entry_points = importlib.metadata.entry_points().select(
- group="ptbench.config"
+ group="mednet.config"
)
entry_point_dict = {k.name: k for k in entry_points}
diff --git a/src/ptbench/scripts/database.py b/src/mednet/scripts/database.py
similarity index 95%
rename from src/ptbench/scripts/database.py
rename to src/mednet/scripts/database.py
index c99f465a4c3600a394284dab182126b6aaae0550..683cad2ede520e1cae8442cdd784fa0984a8687c 100644
--- a/src/ptbench/scripts/database.py
+++ b/src/mednet/scripts/database.py
@@ -20,7 +20,7 @@ def _get_raw_databases() -> dict[str, dict[str, str]]:
containing two string keys:
* ``module``: the full Pythonic module name (e.g.
- ``ptbench.data.montgomery``)
+ ``mednet.data.montgomery``)
* ``datadir``: points to the user-configured data directory for the
current dataset, if set, or ``None`` otherwise.
"""
@@ -68,7 +68,7 @@ def database() -> None:
1. To install a database, set up its data directory ("datadir"). For
example, to setup access to Montgomery files you downloaded locally at
the directory "/path/to/montgomery/files", edit the RC file (typically
- ``$HOME/.config/ptbench.toml``), and add a line like the following:
+ ``$HOME/.config/mednet.toml``), and add a line like the following:
.. code:: toml
@@ -84,7 +84,7 @@ def database() -> None:
.. code:: sh
- $ ptbench database list
+ $ mednet database list
""",
)
@@ -113,7 +113,7 @@ def list():
.. code:: sh
- ptbench datamodule check -vv montgomery-f0
+ mednet datamodule check -vv montgomery-f0
""",
)
@@ -138,7 +138,7 @@ def check(split, limit):
click.secho(f"Checking split `{split}`...", fg="yellow")
try:
- module = importlib.metadata.entry_points(group="ptbench.config")[
+ module = importlib.metadata.entry_points(group="mednet.config")[
split
].module
except KeyError:
diff --git a/src/ptbench/scripts/evaluate.py b/src/mednet/scripts/evaluate.py
similarity index 95%
rename from src/ptbench/scripts/evaluate.py
rename to src/mednet/scripts/evaluate.py
index 72f6b3061feaa012788ad10bd2fc12b18837c74d..2a5a85cb931fd1d28066493b4b37aeb752186235 100644
--- a/src/ptbench/scripts/evaluate.py
+++ b/src/mednet/scripts/evaluate.py
@@ -18,7 +18,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -26,13 +26,13 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- ptbench evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results
+ mednet evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results
2. Runs evaluation on an existing prediction output, tune threshold a priori on the `validation` set:
.. code:: sh
- ptbench evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results --threshold=validation
+ mednet evaluate -vv --predictions=path/to/predictions.json --output-folder=path/to/results --threshold=validation
""",
)
@click.option(
diff --git a/src/ptbench/scripts/experiment.py b/src/mednet/scripts/experiment.py
similarity index 97%
rename from src/ptbench/scripts/experiment.py
rename to src/mednet/scripts/experiment.py
index f75569513efaada033140c1f78c58cf79a19a72a..fb37201bea4e35df3d8ced34daaf6e6528eff4d7 100644
--- a/src/ptbench/scripts/experiment.py
+++ b/src/mednet/scripts/experiment.py
@@ -16,7 +16,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -27,7 +27,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- $ ptbench experiment -vv pasa montgomery --epochs=2
+ $ mednet experiment -vv pasa montgomery --epochs=2
""",
)
@training_options
diff --git a/src/ptbench/scripts/predict.py b/src/mednet/scripts/predict.py
similarity index 93%
rename from src/ptbench/scripts/predict.py
rename to src/mednet/scripts/predict.py
index 6b77f3d3d9d580df59348a45ca9841b19b9ba0a6..828ba4ff9304db9352e73aea1885229f361b0432 100644
--- a/src/ptbench/scripts/predict.py
+++ b/src/mednet/scripts/predict.py
@@ -15,7 +15,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -23,13 +23,13 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- ptbench predict -vv pasa montgomery --weight=path/to/model-at-lowest-validation-loss.ckpt --output=path/to/predictions.json
+ mednet predict -vv pasa montgomery --weight=path/to/model.ckpt --output=path/to/predictions.json
2. Enables multi-processing data loading with 6 processes:
.. code:: sh
- ptbench predict -vv pasa montgomery --parallel=6 --weight=path/to/model-at-lowest-validation-loss.ckpt --output=path/to/predictions.json
+ mednet predict -vv pasa montgomery --parallel=6 --weight=path/to/model.ckpt --output=path/to/predictions.json
""",
)
diff --git a/src/ptbench/scripts/train.py b/src/mednet/scripts/train.py
similarity index 99%
rename from src/ptbench/scripts/train.py
rename to src/mednet/scripts/train.py
index b2663208b3c3bbb2ce9f3c895a49076cb6daf9ba..7c329359a61c7e14d72b360db58ff3852e4141af 100644
--- a/src/ptbench/scripts/train.py
+++ b/src/mednet/scripts/train.py
@@ -220,7 +220,7 @@ def reusable_options(f):
@click.command(
- entry_point_group="ptbench.config",
+ entry_point_group="mednet.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -228,7 +228,7 @@ def reusable_options(f):
.. code:: sh
- ptbench train -vv pasa montgomery --batch-size=4 --device="cuda:0"
+ mednet train -vv pasa montgomery --batch-size=4 --device="cuda:0"
""",
)
@reusable_options
diff --git a/src/ptbench/scripts/train_analysis.py b/src/mednet/scripts/train_analysis.py
similarity index 98%
rename from src/ptbench/scripts/train_analysis.py
rename to src/mednet/scripts/train_analysis.py
index f108f00d722638ae2cc2322e479f72ff6f870ccb..94867b6adf66443ff4adb902573c7482eca9c1da 100644
--- a/src/ptbench/scripts/train_analysis.py
+++ b/src/mednet/scripts/train_analysis.py
@@ -113,7 +113,7 @@ def create_figures(
.. code:: sh
- ptbench train-analysis -vv results/logs
+ mednet train-analysis -vv results/logs
""",
)
@click.argument(
diff --git a/src/ptbench/scripts/utils.py b/src/mednet/scripts/utils.py
similarity index 100%
rename from src/ptbench/scripts/utils.py
rename to src/mednet/scripts/utils.py
diff --git a/src/ptbench/utils/__init__.py b/src/mednet/utils/__init__.py
similarity index 100%
rename from src/ptbench/utils/__init__.py
rename to src/mednet/utils/__init__.py
diff --git a/src/ptbench/utils/checkpointer.py b/src/mednet/utils/checkpointer.py
similarity index 100%
rename from src/ptbench/utils/checkpointer.py
rename to src/mednet/utils/checkpointer.py
diff --git a/src/ptbench/utils/rc.py b/src/mednet/utils/rc.py
similarity index 86%
rename from src/ptbench/utils/rc.py
rename to src/mednet/utils/rc.py
index 21ebda080d481f88fd7b5e0ee07ff9ddcf427516..1a99df49783454a28a7e6dd9692056a5660198b3 100644
--- a/src/ptbench/utils/rc.py
+++ b/src/mednet/utils/rc.py
@@ -7,4 +7,4 @@ from clapper.rc import UserDefaults
def load_rc() -> UserDefaults:
"""Returns global configuration variables."""
- return UserDefaults("ptbench.toml")
+ return UserDefaults("mednet.toml")
diff --git a/src/ptbench/utils/resources.py b/src/mednet/utils/resources.py
similarity index 100%
rename from src/ptbench/utils/resources.py
rename to src/mednet/utils/resources.py
diff --git a/src/ptbench/utils/summary.py b/src/mednet/utils/summary.py
similarity index 100%
rename from src/ptbench/utils/summary.py
rename to src/mednet/utils/summary.py
diff --git a/src/ptbench/utils/tensorboard.py b/src/mednet/utils/tensorboard.py
similarity index 100%
rename from src/ptbench/utils/tensorboard.py
rename to src/mednet/utils/tensorboard.py
diff --git a/tests/conftest.py b/tests/conftest.py
index 82eef6449eb26e93be4ff39b57b420d86cd8a68c..60d00e284ba5656189bbb05b03a3deb5afb549a9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -12,7 +12,7 @@ import pytest
import tomli_w
import torch
-from ptbench.data.typing import DatabaseSplit
+from mednet.data.typing import DatabaseSplit
@pytest.fixture
@@ -26,7 +26,7 @@ def pytest_configure(config):
config.addinivalue_line(
"markers",
"skip_if_rc_var_not_set(name): this mark skips the test if a certain "
- "~/.config/ptbench.toml variable is not set",
+ "~/.config/mednet.toml variable is not set",
)
config.addinivalue_line("markers", "slow: this mark indicates slow tests")
@@ -38,7 +38,7 @@ def pytest_runtest_setup(item):
The test is run if this function returns ``None``. To skip a test,
call ``pytest.skip()``, specifying a reason.
"""
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
@@ -49,19 +49,19 @@ def pytest_runtest_setup(item):
for mark in item.iter_markers(name="skip_if_rc_var_not_set")
]
- # checks all names mentioned are set in ~/.config/ptbench.toml, otherwise,
+ # checks all names mentioned are set in ~/.config/mednet.toml, otherwise,
# skip the test
if rc_names:
missing = [k for k in rc_names if rc.get(k) is None]
if any(missing):
pytest.skip(
f"Test skipped because {', '.join(missing)} is **not** "
- f"set in ~/.config/ptbench.toml"
+ f"set in ~/.config/mednet.toml"
)
def rc_variable_set(name):
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
pytest.mark.skipif(
@@ -79,7 +79,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
"""Presets the session start to ensure the Montgomery dataset is always
available."""
- from ptbench.utils.rc import load_rc
+ from mednet.utils.rc import load_rc
rc = load_rc()
@@ -94,7 +94,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
)
assert archive.exists(), (
f"Neither datadir.montgomery is set on the global configuration, "
- f"(typically ~/.config/ptbench.toml), or it is possible to detect "
+ f"(typically ~/.config/mednet.toml), or it is possible to detect "
f"the presence of {archive}' (did you git submodule init --update "
f"this submodule?)"
)
@@ -105,7 +105,7 @@ def pytest_sessionstart(session: pytest.Session) -> None:
with zipfile.ZipFile(archive) as zf:
zf.extractall(montgomery_tempdir.name)
- config_filename = "ptbench.toml"
+ config_filename = "mednet.toml"
with open(
os.path.join(montgomery_tempdir.name, config_filename), "wb"
) as f:
diff --git a/tests/test_cli.py b/tests/test_cli.py
index f5cf9fa88515b549f91cd692aadec1cc515fdc1a..30e460194a767a8ec20ef6dcc6cda64f26f0aed8 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -24,7 +24,7 @@ def stdout_logging():
ch = logging.StreamHandler(buf)
ch.setFormatter(logging.Formatter("%(message)s"))
ch.setLevel(logging.INFO)
- logger = logging.getLogger("ptbench")
+ logger = logging.getLogger("mednet")
logger.addHandler(ch)
yield buf
logger.removeHandler(ch)
@@ -44,45 +44,45 @@ def _check_help(entry_point):
def test_config_help():
- from ptbench.scripts.config import config
+ from mednet.scripts.config import config
_check_help(config)
def test_config_list_help():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
_check_help(list)
def test_config_list():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
runner = CliRunner()
result = runner.invoke(list)
_assert_exit_0(result)
- assert "module: ptbench.config.data" in result.output
- assert "module: ptbench.config.models" in result.output
+ assert "module: mednet.config.data" in result.output
+ assert "module: mednet.config.models" in result.output
def test_config_list_v():
- from ptbench.scripts.config import list
+ from mednet.scripts.config import list
result = CliRunner().invoke(list, ["--verbose"])
_assert_exit_0(result)
- assert "module: ptbench.config.data" in result.output
- assert "module: ptbench.config.models" in result.output
+ assert "module: mednet.config.data" in result.output
+ assert "module: mednet.config.models" in result.output
def test_config_describe_help():
- from ptbench.scripts.config import describe
+ from mednet.scripts.config import describe
_check_help(describe)
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_config_describe_montgomery():
- from ptbench.scripts.config import describe
+ from mednet.scripts.config import describe
runner = CliRunner()
result = runner.invoke(describe, ["montgomery"])
@@ -91,19 +91,19 @@ def test_config_describe_montgomery():
def test_database_help():
- from ptbench.scripts.database import database
+ from mednet.scripts.database import database
_check_help(database)
def test_datamodule_list_help():
- from ptbench.scripts.database import list
+ from mednet.scripts.database import list
_check_help(list)
def test_datamodule_list():
- from ptbench.scripts.database import list
+ from mednet.scripts.database import list
runner = CliRunner()
result = runner.invoke(list)
@@ -112,14 +112,14 @@ def test_datamodule_list():
def test_datamodule_check_help():
- from ptbench.scripts.database import check
+ from mednet.scripts.database import check
_check_help(check)
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_database_check():
- from ptbench.scripts.database import check
+ from mednet.scripts.database import check
runner = CliRunner()
result = runner.invoke(check, ["--verbose", "--limit=1", "montgomery"])
@@ -127,13 +127,13 @@ def test_database_check():
def test_main_help():
- from ptbench.scripts.cli import cli
+ from mednet.scripts.cli import cli
_check_help(cli)
def test_train_help():
- from ptbench.scripts.train import train
+ from mednet.scripts.train import train
_check_help(train)
@@ -143,13 +143,13 @@ def _str_counter(substr, s):
def test_predict_help():
- from ptbench.scripts.predict import predict
+ from mednet.scripts.predict import predict
_check_help(predict)
def test_evaluate_help():
- from ptbench.scripts.evaluate import evaluate
+ from mednet.scripts.evaluate import evaluate
_check_help(evaluate)
@@ -180,8 +180,8 @@ def test_saliency_evaluate_help():
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery(temporary_basedir):
- from ptbench.scripts.train import train
- from ptbench.utils.checkpointer import (
+ from mednet.scripts.train import train
+ from mednet.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
@@ -245,8 +245,8 @@ def test_train_pasa_montgomery(temporary_basedir):
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
- from ptbench.scripts.train import train
- from ptbench.utils.checkpointer import (
+ from mednet.scripts.train import train
+ from mednet.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
@@ -343,8 +343,8 @@ def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_predict_pasa_montgomery(temporary_basedir, datadir):
- from ptbench.scripts.predict import predict
- from ptbench.utils.checkpointer import (
+ from mednet.scripts.predict import predict
+ from mednet.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
@@ -395,7 +395,7 @@ def test_predict_pasa_montgomery(temporary_basedir, datadir):
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_evaluate_pasa_montgomery(temporary_basedir):
- from ptbench.scripts.evaluate import evaluate
+ from mednet.scripts.evaluate import evaluate
runner = CliRunner()
@@ -479,7 +479,7 @@ def test_evaluate_pasa_montgomery(temporary_basedir):
# @pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
# def test_predict_densenetrs_montgomery(temporary_basedir, datadir):
-# from ptbench.scripts.predict import predict
+# from mednet.scripts.predict import predict
# runner = CliRunner()
diff --git a/tests/test_database_split.py b/tests/test_database_split.py
index aa360e2c889952d976252aac68725dbc6ced1095..f7d8d3403f20f9e2fbd609e9e438b442bfbdb9e4 100644
--- a/tests/test_database_split.py
+++ b/tests/test_database_split.py
@@ -3,7 +3,7 @@
# SPDX-License-Identifier: GPL-3.0-or-later
"""Test code for datasets."""
-from ptbench.data.split import CSVDatabaseSplit, JSONDatabaseSplit
+from mednet.data.split import CSVDatabaseSplit, JSONDatabaseSplit
def test_csv_loading(datadir):
diff --git a/tests/test_evaluator.py b/tests/test_evaluator.py
index 5394dc6fa0b36b5f496ac71271381243854e084c..1fc4ae635cf426bed9ededb502530ed0d2acb6c0 100644
--- a/tests/test_evaluator.py
+++ b/tests/test_evaluator.py
@@ -7,7 +7,7 @@ import numpy
def test_centered_maxf1():
- from ptbench.engine.evaluator import _get_centered_maxf1
+ from mednet.engine.evaluator import _get_centered_maxf1
# Multiple max F1
f1_scores = numpy.array([0.8, 0.9, 1.0, 1.0, 1.0, 0.3])
diff --git a/tests/test_hivtb.py b/tests/test_hivtb.py
index 1311981205cb44aa11d157f4f3b0fde1a4f3629a..00b7a484beda022cebde19a71cf272a16b1cb12c 100644
--- a/tests/test_hivtb.py
+++ b/tests/test_hivtb.py
@@ -33,7 +33,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.hivtb.datamodule import make_split
+ from mednet.config.data.hivtb.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -69,7 +69,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.hivtb"
+ f".{name}", "mednet.config.data.hivtb"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_image_utils.py b/tests/test_image_utils.py
index 420fdf043bc9fe7bba1ee223b685698ee3010e03..57317c22a108c0b953f348b5adf7a450ff5e88d6 100644
--- a/tests/test_image_utils.py
+++ b/tests/test_image_utils.py
@@ -6,7 +6,7 @@
import numpy
import PIL.Image
-from ptbench.data.image_utils import remove_black_borders
+from mednet.data.image_utils import remove_black_borders
def test_remove_black_borders(datadir):
diff --git a/tests/test_indian.py b/tests/test_indian.py
index e86b56f6e3b847cc4751435e8947264ae571e868..66ffdef3c5e0cbc570fd8b5020279cc8ef755c4f 100644
--- a/tests/test_indian.py
+++ b/tests/test_indian.py
@@ -37,7 +37,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.indian.datamodule import make_split
+ from mednet.config.data.indian.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -74,7 +74,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_montgomery.py b/tests/test_montgomery.py
index 1e8227d33e68f8f112e910af9a9a5ec7fbb273bd..6933e9825c7398bb0c6b65b7f37794a98aa11cc7 100644
--- a/tests/test_montgomery.py
+++ b/tests/test_montgomery.py
@@ -34,7 +34,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.montgomery.datamodule import make_split
+ from mednet.config.data.montgomery.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -71,7 +71,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_montgomery_shenzhen.py b/tests/test_montgomery_shenzhen.py
index 9af425a57873314e85861e62195dc7c13b4b94a1..7f7119054299e7552c567d9df7cb45c7f8d9d028 100644
--- a/tests/test_montgomery_shenzhen.py
+++ b/tests/test_montgomery_shenzhen.py
@@ -26,23 +26,23 @@ import pytest
)
def test_split_consistency(name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen"
+ f".{name}", "mednet.config.data.montgomery_shenzhen"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian.py b/tests/test_montgomery_shenzhen_indian.py
index b3c7f5f511ad82e2c279d4dbd5a0cb585f6fa4d8..3134574e5b665cceeb48f80bf5806c436af5d44b 100644
--- a/tests/test_montgomery_shenzhen_indian.py
+++ b/tests/test_montgomery_shenzhen_indian.py
@@ -26,31 +26,31 @@ import pytest
)
def test_split_consistency(name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen_indian"
+ f".{name}", "mednet.config.data.montgomery_shenzhen_indian"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian_padchest.py b/tests/test_montgomery_shenzhen_indian_padchest.py
index 95b59bf14344502ae57240af195a3a898df7a5ec..84b0aca9eff04d2d5f54e1236ae1028df2204e3c 100644
--- a/tests/test_montgomery_shenzhen_indian_padchest.py
+++ b/tests/test_montgomery_shenzhen_indian_padchest.py
@@ -16,39 +16,39 @@ import pytest
)
def test_split_consistency(name: str, padchest_name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.config.data.padchest"
+ f".{padchest_name}", "mednet.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery_shenzhen_indian_padchest"
+ f".{name}", "mednet.config.data.montgomery_shenzhen_indian_padchest"
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.padchest"
+ ".datamodule", "mednet.config.data.padchest"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_montgomery_shenzhen_indian_tbx11k.py b/tests/test_montgomery_shenzhen_indian_tbx11k.py
index 71956b49d95808112de052e68bea8859c33742a1..d38cd77a2e845bb2d863e26f5e9517935e545ca8 100644
--- a/tests/test_montgomery_shenzhen_indian_tbx11k.py
+++ b/tests/test_montgomery_shenzhen_indian_tbx11k.py
@@ -37,40 +37,40 @@ import pytest
)
def test_split_consistency(name: str, tbx11k_name: str):
montgomery = importlib.import_module(
- f".{name}", "ptbench.config.data.montgomery"
+ f".{name}", "mednet.config.data.montgomery"
).datamodule
shenzhen = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
indian = importlib.import_module(
- f".{name}", "ptbench.config.data.indian"
+ f".{name}", "mednet.config.data.indian"
).datamodule
tbx11k = importlib.import_module(
- f".{tbx11k_name}", "ptbench.config.data.tbx11k"
+ f".{tbx11k_name}", "mednet.config.data.tbx11k"
).datamodule
combined = importlib.import_module(
f".{tbx11k_name}",
- "ptbench.config.data.montgomery_shenzhen_indian_tbx11k",
+ "mednet.config.data.montgomery_shenzhen_indian_tbx11k",
).datamodule
MontgomeryLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.montgomery"
+ ".datamodule", "mednet.config.data.montgomery"
).RawDataLoader
ShenzhenLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.shenzhen"
+ ".datamodule", "mednet.config.data.shenzhen"
).RawDataLoader
IndianLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.indian"
+ ".datamodule", "mednet.config.data.indian"
).RawDataLoader
TBX11kLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.tbx11k"
+ ".datamodule", "mednet.config.data.tbx11k"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_nih_cxr14.py b/tests/test_nih_cxr14.py
index 83f4521284cfae963f1f2f5a5e286015d1f15d63..8188c7cb3d3650b71a445fba484b40369c283f52 100644
--- a/tests/test_nih_cxr14.py
+++ b/tests/test_nih_cxr14.py
@@ -25,7 +25,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.nih_cxr14.datamodule import make_split
+ from mednet.config.data.nih_cxr14.datamodule import make_split
database_checkers.check_split(
make_split(split),
@@ -52,7 +52,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.nih_cxr14"
+ f".{name}", "mednet.config.data.nih_cxr14"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_nih_cxr14_padchest.py b/tests/test_nih_cxr14_padchest.py
index 5c5bb5efccec30de0369cd24822d86de44e37978..2c013398690a367b0c9c184f7710a05f345424e4 100644
--- a/tests/test_nih_cxr14_padchest.py
+++ b/tests/test_nih_cxr14_padchest.py
@@ -16,23 +16,23 @@ import pytest
)
def test_split_consistency(name: str, padchest_name: str, combined_name: str):
nih_cxr14 = importlib.import_module(
- f".{name}", "ptbench.config.data.nih_cxr14"
+ f".{name}", "mednet.config.data.nih_cxr14"
).datamodule
padchest = importlib.import_module(
- f".{padchest_name}", "ptbench.config.data.padchest"
+ f".{padchest_name}", "mednet.config.data.padchest"
).datamodule
combined = importlib.import_module(
- f".{combined_name}", "ptbench.config.data.nih_cxr14_padchest"
+ f".{combined_name}", "mednet.config.data.nih_cxr14_padchest"
).datamodule
CXR14Loader = importlib.import_module(
- ".datamodule", "ptbench.config.data.nih_cxr14"
+ ".datamodule", "mednet.config.data.nih_cxr14"
).RawDataLoader
PadChestLoader = importlib.import_module(
- ".datamodule", "ptbench.config.data.padchest"
+ ".datamodule", "mednet.config.data.padchest"
).RawDataLoader
for split in ("train", "validation", "test"):
diff --git a/tests/test_padchest.py b/tests/test_padchest.py
index 54b42b6d3ac29bf582929d0180de84a56f6bd962..dfa491c879880ec01126dc11e4a112f775abaac0 100644
--- a/tests/test_padchest.py
+++ b/tests/test_padchest.py
@@ -30,7 +30,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.padchest.datamodule import make_split
+ from mednet.config.data.padchest.datamodule import make_split
database_checkers.check_split(
make_split(split),
@@ -56,7 +56,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.padchest"
+ f".{name}", "mednet.config.data.padchest"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_shenzhen.py b/tests/test_shenzhen.py
index b45ce0dbbdd26f7d55ec77d90e6c6a489dfa32c2..6658831bdcb973aaa095385af28418d9ec4b2297 100644
--- a/tests/test_shenzhen.py
+++ b/tests/test_shenzhen.py
@@ -34,7 +34,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.shenzhen.datamodule import make_split
+ from mednet.config.data.shenzhen.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -71,7 +71,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.shenzhen"
+ f".{name}", "mednet.config.data.shenzhen"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_summary.py b/tests/test_summary.py
index 0f3a76899833185642387c2fc0aded238441b1b3..09b5398abda79804ef2fcbf6b1b191d9310dcb29 100644
--- a/tests/test_summary.py
+++ b/tests/test_summary.py
@@ -4,9 +4,9 @@
import unittest
-import ptbench.config.models.pasa as pasa_config
+import mednet.config.models.pasa as pasa_config
-from ptbench.utils.summary import summary
+from mednet.utils.summary import summary
class Tester(unittest.TestCase):
diff --git a/tests/test_tbpoc.py b/tests/test_tbpoc.py
index cf3327d4afbea2aeb5b73deca4d5c27cd9305967..a2704fa71c1006bc42a28c3facd0843cc4698ba7 100644
--- a/tests/test_tbpoc.py
+++ b/tests/test_tbpoc.py
@@ -33,7 +33,7 @@ def id_function(val):
def test_protocol_consistency(
database_checkers, split: str, lenghts: dict[str, int]
):
- from ptbench.config.data.tbpoc.datamodule import make_split
+ from mednet.config.data.tbpoc.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -72,7 +72,7 @@ def test_protocol_consistency(
)
def test_loading(database_checkers, name: str, dataset: str):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.tbpoc"
+ f".{name}", "mednet.config.data.tbpoc"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_tbx11k.py b/tests/test_tbx11k.py
index e7dae5678b1cc3ff18cc728a485f33d730de24f6..71c37e1615b48eb96955a82782188d5223c2a296 100644
--- a/tests/test_tbx11k.py
+++ b/tests/test_tbx11k.py
@@ -138,7 +138,7 @@ def test_protocol_consistency(
lenghts: dict[str, int],
prefixes: typing.Sequence[str],
):
- from ptbench.config.data.tbx11k.datamodule import make_split
+ from mednet.config.data.tbx11k.datamodule import make_split
database_checkers.check_split(
make_split(f"{split}.json"),
@@ -251,7 +251,7 @@ def check_loaded_batch(
)
def test_loading(name: str, dataset: str, prefixes: typing.Sequence[str]):
datamodule = importlib.import_module(
- f".{name}", "ptbench.config.data.tbx11k"
+ f".{name}", "mednet.config.data.tbx11k"
).datamodule
datamodule.model_transforms = [] # should be done before setup()
diff --git a/tests/test_transforms.py b/tests/test_transforms.py
index 2c324aa1691d897c6acb0f9c71e7bd4f9d2cb089..651c4123cbafefa4837411531c2584e74f0ea077 100644
--- a/tests/test_transforms.py
+++ b/tests/test_transforms.py
@@ -7,7 +7,7 @@ import numpy
import PIL.Image
import torchvision.transforms.functional as F
-from ptbench.data.augmentations import ElasticDeformation
+from mednet.data.augmentations import ElasticDeformation
def test_elastic_deformation(datadir):