diff --git a/README.md b/README.md index 5ac5fc52bd854d322d8a0419c4c02d5e130711db..810b740dfcc9a300a220d78c6a7a885c970ecd30 100644 --- a/README.md +++ b/README.md @@ -8,9 +8,10 @@ SPDX-License-Identifier: GPL-3.0-or-later [](https://www.idiap.ch/software/biosignal/docs/biosignal/software/ptbench/main/coverage/index.html) [](https://gitlab.idiap.ch/biosignal/software/ptbench) -# Active Pulmonary Tuberculosis Detection On Chest X-Rays +# Computer-Aided Disease Detection from Medical Data -Benchmarks for training and evaluating deep models for the detection of active -Pulmonary Tuberculosis from Chest X-Ray imaging. +Benchmarks of convolutional neural network (CNN) architectures applied to +disease detection, including Pulmonary Tuberculosis (TB) detection on chest +X-rays (CXR). For installation and usage instructions, check-out our documentation. diff --git a/doc/index.rst b/doc/index.rst index 964e4f35d4916227ca78b731b1d87acc3d1d89d3..e948754e9e4351b23f3ab668b93f9c46790cd400 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -4,14 +4,15 @@ .. _ptbench: -========================================================= - Active Pulmonary Tuberculosis Detection On Chest X-Rays -========================================================= +==================================================== + Computer-Aided Disease Detection from Medical Data +==================================================== .. todolist:: Benchmarks of convolutional neural network (CNN) architectures applied to -Pulmonary Tuberculosis (TB) detection on chest X-rays (CXR). +disease detection, including Pulmonary Tuberculosis (TB) detection on chest +X-rays (CXR). Please use the BibTeX reference below to cite this work: diff --git a/pyproject.toml b/pyproject.toml index 8ebe16e4e5b18a26930ce3439a740c79e17cb980..30741ef8665a4e595d2aa88e524b1b57f95f3c50 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta" name = "ptbench" version = "1.0.0b0" requires-python = ">=3.10" -description = "Benchmarks for training and evaluating deep models for the detection of active Pulmonary Tuberculosis from Chest X-Ray imaging." +description = "Benchmarks for Computer-Aided Disease Detection from Medical Data." dynamic = ["readme"] license = { text = "GNU General Public License v3 (GPLv3)" } authors = [{ name = "Geoffrey Raposo", email = "geoffrey@raposo.ch" }] diff --git a/src/ptbench/scripts/cli.py b/src/ptbench/scripts/cli.py index 3b27fe7819359c97f5cd1ab8d6a9e3f8fcbf09d7..11cba171fb6857ca3e6fe08e2c355ab12e429f0a 100644 --- a/src/ptbench/scripts/cli.py +++ b/src/ptbench/scripts/cli.py @@ -22,7 +22,7 @@ from . import ( context_settings=dict(help_option_names=["-?", "-h", "--help"]), ) def cli(): - """Active Tuberculosis Detection On Chest X-Ray Images.""" + """Image classification benchmark.""" pass diff --git a/src/ptbench/scripts/evaluate.py b/src/ptbench/scripts/evaluate.py index 19afc037c4dfaa11a0f5fa32628cb08602b52b49..2e4fe626fbba296b030c82effc53390924096dbc 100644 --- a/src/ptbench/scripts/evaluate.py +++ b/src/ptbench/scripts/evaluate.py @@ -11,6 +11,9 @@ from clapper.logging import setup from .click import ConfigCommand +# avoids X11/graphical desktop requirement when creating plots +__import__("matplotlib").use("agg") + logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s") @@ -76,7 +79,7 @@ def evaluate( threshold: str | float, **_, # ignored ) -> None: - """Evaluates predictions (from a model) on a binary classification task.""" + """Evaluates predictions (from a model) on a classification task.""" import json import typing diff --git a/src/ptbench/scripts/experiment.py b/src/ptbench/scripts/experiment.py index fdac41a2c5bf3873862486f97a006375123fa48d..55c24260f5d32271ed74705b77b07b6a311bb39a 100644 --- a/src/ptbench/scripts/experiment.py +++ b/src/ptbench/scripts/experiment.py @@ -9,6 +9,9 @@ from clapper.logging import setup from .train import reusable_options as training_options +# avoids X11/graphical desktop requirement when creating plots +__import__("matplotlib").use("agg") + logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s") diff --git a/src/ptbench/scripts/predict.py b/src/ptbench/scripts/predict.py index 0b54d05146cbbb6fceffd5e58f6928e0580cb1d5..054590e2631b462ec11e78ea73e16a6a7858cb89 100644 --- a/src/ptbench/scripts/predict.py +++ b/src/ptbench/scripts/predict.py @@ -117,7 +117,8 @@ def predict( parallel, **_, ) -> None: - """Predicts Tuberculosis presence (probabilities) on input images.""" + """Runs inference (generates scores) on all input images, using a pre- + trained model.""" import json import shutil