auditapp 0.0.7__tar.gz

auditapp-0.0.7/LICENSE.md

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auditapp-0.0.7/PKG-INFO

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+Metadata-Version: 2.1
+Name: auditapp
+Version: 0.0.7
+Summary: AUDIT, Analysis & evalUation Dashboard of artIficial inTelligence
+Home-page: https://github.com/caumente/AUDIT
+License: Apache-2.0
+Keywords: medical image analysis,deep learning,mri,model evaluation,dashboard
+Author: Carlos Aumente
+Author-email: carlosaumente@gmail.com
+Requires-Python: >=3.10,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Dist: click (>=8.0,<9.0)
+Requires-Dist: colorama (==0.4.6)
+Requires-Dist: loguru (==0.7.2)
+Requires-Dist: matplotlib (==3.5.3)
+Requires-Dist: numpy (==1.26.4)
+Requires-Dist: pandas (==1.3.5)
+Requires-Dist: pillow (==10.4.0)
+Requires-Dist: plotly (==5.22.0)
+Requires-Dist: pymia (==0.3.2)
+Requires-Dist: pyyaml (==6.0.2)
+Requires-Dist: scikit-image (==0.25.0)
+Requires-Dist: scipy (==1.13.1)
+Requires-Dist: simpleitk (==2.3.1)
+Requires-Dist: statsmodels (==0.14.0)
+Requires-Dist: stqdm (==0.0.5)
+Requires-Dist: streamlit (==1.32.0)
+Requires-Dist: streamlit-plotly-events (==0.0.6)
+Requires-Dist: tqdm (==4.64.0)
+Project-URL: Documentation, https://caumente.github.io/AUDIT/
+Project-URL: Repository, https://github.com/caumente/AUDIT
+Description-Content-Type: text/markdown
+
+
+[//]: # (![alt text]&#40;https://github.com/caumente/AUDIT/blob/main/src/app/util/images/AUDIT_big.jpeg&#41;)
+![alt text](https://github.com/caumente/AUDIT/blob/main/src/app/util/images/AUDIT_medium.jpeg)
+
+
+<a href="https://github.com/caumente/AUDIT" title="Go to GitHub repo"><img src="https://img.shields.io/static/v1?label=caumente&message=AUDIT&color=e78ac3&logo=github" alt="caumente - AUDIT"></a>
+<a href="https://github.com/caumente/AUDIT"><img src="https://img.shields.io/github/stars/caumente/AUDIT?style=social" alt="stars - AUDIT"></a>
+<a href="https://github.com/caumente/AUDIT"><img src="https://img.shields.io/github/forks/caumente/AUDIT?style=social" alt="forks - AUDIT"></a>
+
+
+<a href="https://github.com/caumente/audit/releases/"><img src="https://img.shields.io/github/release/caumente/audit?include_prereleases=&sort=semver&color=e78ac3" alt="GitHub release"></a>
+<a href="#license"><img src="https://img.shields.io/badge/License-Apache_2.0-e78ac3" alt="License"></a>
+<a href="https://github.com/caumente/audit/issues"><img src="https://img.shields.io/github/issues/caumente/audit" alt="issues - AUDIT"></a>
+
+
+## Summary
+
+AUDIT, Analysis & evalUation Dashboard of artIficial inTelligence, is a tool designed to analyze,
+visualize, and detect biases in brain MRI data and models. It provides tools for loading and processing MRI data,
+extracting relevant features, and visualizing model performance and biases in predictions. AUDIT presents the 
+following features:
+
+
+- **Data management**: Easily work with MRI data from various sources.
+- **Feature extraction**: Extract relevant features from MRI images and their segmentations for analysis.
+- **Visualization**: Visualize model performance, including false positives and negatives, using interactive plots.
+- **Model robustness**: Assess the robustness of the model by evaluating its performance across different datasets and conditions.
+- **Bias detection**: Identify potential biases in model predictions and performance.
+- **Longitudinal analysis**: Track your model performance over different time points.
+
+Details of our work are provided in [*our paper*](...........), **AUDIT**. We hope that 
+users will use *AUDIT* to gain novel insights into brain tumor segmentation field. 
+
+
+## Usage
+- **Home Page**: The main landing page of the tool.
+- **Univariate Analysis**: Analysis of individual variables to understand their distributions and characteristics.
+- **Multivariate Analysis**: Examination of multiple variables simultaneously to explore relationships and patterns.
+- **Segmentation Error Matrix**: A table displaying the errors associated with different segmentation tasks.
+- **Model Performance Analysis**: Evaluation of the effectiveness and accuracy of a single model.
+- **Pairwise Model Performance Comparison**: Comparison of performance metrics between two different models.
+- **Multi-model Performance Comparison**: Comparative analysis of performance metrics across multiple models.
+- **Longitudinal Measurements**: Analysis of data collected over time to observe trends and changes.
+- **Subjects Exploration**: Detailed examination of individual subjects within the dataset.
+
+
+## Web AUDIT
+
+Last released version of **AUDIT** is hosted at https://audit.streamlitapp.com for an online overview of its functionalities.
+
+
+## Getting Started
+
+### 1.1 Installation via PIP installer (Not available yet)
+
+```bash
+pip install audit
+```
+
+### 1.2. Installation via AUDIT repository 
+
+### 1.2.1. Using Anaconda
+(Recommended) Create an isolated Anaconda environment:
+
+```bash
+conda create -n audit_env python=3.10
+conda activate audit_env
+```
+
+Clone the repository:
+ ```bash
+ git clone https://github.com/caumente/AUDIT.git
+ cd AUDIT
+ ```
+
+Install the required packages:
+ ```bash
+ pip install -r requirements.txt
+ ```
+
+### 1.2.2 Using Poetry
+
+The library _poetry_ must be installed in your environment to follow this via of installation.
+
+Clone the repository:
+ ```bash
+ git clone git@github.com:caumente/AUDIT.git
+ cd AUDIT
+```
+
+Install the dependencies:
+```bash
+poetry install
+```
+
+Activate virtual environment:
+```bash
+poetry shell
+```
+
+
+### 2. Configuration
+
+Edit the config files in `./src/configs/` directory to set up the paths for data loading and other configurations:
+
+
+<details>
+  <summary><strong>2.1. Feature extractor config</strong></summary>
+
+```yaml
+# Paths to all the datasets
+data_paths:
+  dataset_1: '/home/user/AUDIT/datasets/dataset_1/dataset_1_images'
+  dataset_N: '/home/user/AUDIT/datasets/dataset_N/dataset_N_images'
+
+# Mapping of labels to their numeric values
+labels:
+  BKG: 0
+  EDE: 3
+  ENH: 1
+  NEC: 2
+
+# List of features to extract
+features:
+  statistical: true
+  texture: false
+  spatial: false
+  tumor: false
+
+# Longitudinal study settings
+#longitudinal:
+#  dataset_N:
+#    pattern: "_"            # Pattern used for splitting filename
+#    longitudinal_id: 1      # Index position for the subject ID after splitting the filename
+#    time_point: 2           # Index position for the time point after splitting the filename
+
+
+# Path where extracted features will be saved
+output_path: '/home/user/AUDIT/outputs/features'
+```
+</details>
+
+
+<details>
+  <summary><strong>2.2. Metric extractor config</strong></summary>
+
+```yaml
+# Path to the raw dataset
+data_path: '/home/carlos/AUDIT/datasets/dataset_1/dataset_1_images'
+
+# Paths to model predictions
+model_predictions_paths:
+  model_1: '/home/user/AUDIT/datasets/dataset_1/dataset_1_seg/model_1'
+  model_M: '/home/user/AUDIT/datasets/dataset_1/dataset_1_seg/model_M'
+
+# Mapping of labels to their numeric values
+labels:
+  BKG: 0
+  EDE: 3
+  ENH: 1
+  NEC: 2
+
+# List of metrics to compute
+metrics:
+  dice: true
+  jacc: false
+  accu: false
+  prec: false
+  sens: false
+  spec: false
+  haus: false
+
+# Library used for computing all the metrics
+package: custom
+calculate_stats: false
+
+# Path where output metrics will be saved
+output_path: '/home/user/AUDIT/outputs/metrics'
+
+# Filename for the extracted information
+filename: 'dataset_1'
+```
+</details>
+
+
+<details>
+  <summary><strong>2.3. APP config</strong></summary>
+
+```yaml
+# Mapping of labels to their numeric values
+labels:
+  BKG: 0
+  EDE: 3
+  ENH: 1
+  NEC: 2
+
+# Root path for datasets, features extracted, and metrics extracted
+datasets_path: '/home/user/AUDIT/datasets'
+features_path: '/home/user/AUDIT/outputs/features'
+metrics_path: '/home/user/AUDIT/outputs/metrics'
+
+# Paths for raw datasets
+raw_datasets:
+  dataset_1: "${datasets_path}/dataset_1/dataset_1_images"
+  dataset_N: "${datasets_path}/dataset_N/dataset_N_images"
+
+# Paths for feature extraction CSV files
+features:
+  dataset_1: "${features_path}/extracted_information_dataset_1.csv"
+  dataset_N: "${features_path}/extracted_information_dataset_N.csv"
+
+# Paths for metric extraction CSV files
+metrics:
+  dataset_1: "${metrics_path}/extracted_information_dataset_1.csv"
+  dataset_N: "${metrics_path}/extracted_information_dataset_N.csv"
+
+# Paths for models predictions
+predictions:
+  dataset_1:
+    model_1: "${datasets_path}/dataset_1/dataset_1_seg/model_1"
+    model_M: "${datasets_path}/dataset_1/dataset_1_seg/model_M"
+  dataset_N:
+    model_1: "${datasets_path}/dataset_N/dataset_N_seg/model_1"
+    model_M: "${datasets_path}/dataset_N/dataset_N_seg/model_M"
+```
+</details>
+
+
+### 3. Run AUDIT backend
+
+Use the following commands to run the *Feature extractor* and *Metric extractor* scripts:
+
+```bash
+python src/feature_extractor.py
+```
+
+```bash
+python src/metric_extractor.py
+```
+
+A _logs_ folder will be created after running each of the scripts to keep track of the execution. All the output files 
+will be stored in the folder defined in the corresponding config file (by default in the _output_ folder).
+
+### 4. Run AUDIT app
+
+Use the following streamlit command to run the APP and start the data exploration:
+
+```bash
+streamlit run src/app/APP.py
+```
+
+### 5. Additional configurations
+
+#### 5.1. ITK-Snap
+
+AUDIT is prepared for opening cases with ITK-Snap while exploring the data in the different dashboards. However, the 
+ITK-Snap tool must have been installed and preconfigured before. Here we provide a simple necessary configuration to 
+use it in each operative system:
+
+<details>
+  <summary><strong>5.1.1. On Mac OS</strong></summary>
+
+```bash
+```
+</details>
+
+
+<details>
+  <summary><strong>5.1.2. On Linux OS</strong></summary>
+
+```bash
+```
+</details>
+
+
+
+## Authors
+
+Please feel free to contact us with any issues, comments, or questions.
+
+#### Carlos Aumente 
+
+- Email: <UO297103@uniovi.es>
+- GitHub: https://github.com/caumente
+
+#### Mauricio Reyes 
+#### Michael Muller 
+#### Jorge Díez 
+#### Beatriz Remeseiro 
+
+## License
+Apache License 2.0
+
+
+
+
+
+