jale 0.1.2__tar.gz

jale-0.1.2/JALE.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: jale
+Version: 0.1.2
+Summary: Package allowing users to run Activation Likelihood Estimation Meta-Analysis
+Home-page: https://github.com/LenFrahm/JALE
+Author: Lennart Frahm
+Author-email: l.frahm@mailbox.org
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: customtkinter>=5.2.2
+Requires-Dist: joblib>=1.3.2
+Requires-Dist: nibabel>=5.3.2
+Requires-Dist: numpy>=2.1.2
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pytest>=8.0.0
+Requires-Dist: PyYAML>=6.0.2
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: xgboost>=2.1.2
+Requires-Dist: openpyxl>=3.1.5
+
+# JALE
+
+A Python package for conducting ALE (Activation Likelihood Estimation) meta-analyses, supporting a range of analysis workflows: standard ALE, probabilistic or cross-validated ALE, standard ALE contrast, and balanced ALE contrast.
+
+## Table of Contents
+- [Installation](#installation)
+- [Usage](#usage)
+- [Features](#features)
+- [Examples](#examples)
+- [Background and References](#background-and-references)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+To install the ALE Meta-Analysis Package, run:
+
+```bash
+pip install jale
+```
+## Usage
+
+Here’s how to use the project:
+
+JALE requires a project folder that contains 3 files:
+1. Experiment Data (Author, Subjects, Coordinates, Tags)
+2. Analysis Data (Type of ALE, Tags to be included)
+3. Yaml config file (specifying project folder path, filenames and ALE parameters)
+
+For example files please check the docs folder.
+
+Running an ALE can be done in two ways:
+
+1. via CLI: 
+
+```bash
+python -m jale /path/to/yaml/file
+```
+
+2. in Python:
+
+```python
+from jale import main
+
+main(yaml_path='/path/to/yaml/file')
+```
+
+## Features
+
+- Standard ("Main Effect") ALE: Brief description
+- Probabilistic ("Cross-Validated") ALE: Brief description
+- Standard ALE Contrast: Brief description
+- Balanced ALE Contrast: Brief description
+
+## Background and References
+
+This project is based on research by 
+- [Eickhoff et al., 2012](https://doi.org/10.1016/j.neuroimage.2011.09.017).
+- [Eickhoff et al., 2016](https://doi.org/10.1016/j.neuroimage.2016.04.072).
+- [Frahm et al., 2022](https://doi.org/10.1002/hbm.25898).
+- [Frahm et al., 2023](https://doi.org/10.1016/j.neuroimage.2023.120383).

jale-0.1.2/JALE.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+JALE.egg-info/PKG-INFO
+JALE.egg-info/SOURCES.txt
+JALE.egg-info/dependency_links.txt
+JALE.egg-info/requires.txt
+JALE.egg-info/top_level.txt
+jale/__init__.py
+jale/__main__.py
+jale/ale.py
+jale/ale_gui.py
+jale.egg-info/PKG-INFO
+jale.egg-info/SOURCES.txt
+jale.egg-info/dependency_links.txt
+jale.egg-info/requires.txt
+jale.egg-info/top_level.txt
+jale/assets/__init__.py
+jale/assets/ascii_logo.py
+jale/core/__init__.py
+jale/core/analyses/__init__.py
+jale/core/analyses/clustering.py
+jale/core/analyses/contrast.py
+jale/core/analyses/main_effect.py
+jale/core/analyses/roi.py
+jale/core/utils/__init__.py
+jale/core/utils/compile_experiments.py
+jale/core/utils/compute.py
+jale/core/utils/contribution.py
+jale/core/utils/cutoff_prediction.py
+jale/core/utils/folder_setup.py
+jale/core/utils/input.py
+jale/core/utils/kernel.py
+jale/core/utils/plot_and_save.py
+jale/core/utils/tal2icbm_spm.py
+jale/core/utils/template.py
+jale/core/utils/tfce_par.py
+jale/gui/__init__.py
+jale/gui/add_analysis_window.py
+jale/gui/analysis_table_frame.py
+jale/gui/controller.py
+jale/gui/dataset_table_frame.py
+jale/gui/output_frame.py
+jale/gui/output_log_frame.py
+jale/gui/parameter_window.py
+jale/gui/sidebar_frame.py
+jale/gui/tooltip.py
+tests/__init__.py
+tests/test_input_utils.py
+tests/utils.py

jale-0.1.2/JALE.egg-info/dependency_links.txt

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+

jale-0.1.2/JALE.egg-info/requires.txt

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+customtkinter>=5.2.2
+joblib>=1.3.2
+nibabel>=5.3.2
+numpy>=2.1.2
+pandas>=2.2.3
+pytest>=8.0.0
+PyYAML>=6.0.2
+scipy>=1.14.1
+xgboost>=2.1.2
+openpyxl>=3.1.5

jale-0.1.2/JALE.egg-info/top_level.txt

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+jale
+tests

jale-0.1.2/LICENSE

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+MIT License
+
+Copyright (c) 2024 Lennart Frahm
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

jale-0.1.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: jale
+Version: 0.1.2
+Summary: Package allowing users to run Activation Likelihood Estimation Meta-Analysis
+Home-page: https://github.com/LenFrahm/JALE
+Author: Lennart Frahm
+Author-email: l.frahm@mailbox.org
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: customtkinter>=5.2.2
+Requires-Dist: joblib>=1.3.2
+Requires-Dist: nibabel>=5.3.2
+Requires-Dist: numpy>=2.1.2
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pytest>=8.0.0
+Requires-Dist: PyYAML>=6.0.2
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: xgboost>=2.1.2
+Requires-Dist: openpyxl>=3.1.5
+
+# JALE
+
+A Python package for conducting ALE (Activation Likelihood Estimation) meta-analyses, supporting a range of analysis workflows: standard ALE, probabilistic or cross-validated ALE, standard ALE contrast, and balanced ALE contrast.
+
+## Table of Contents
+- [Installation](#installation)
+- [Usage](#usage)
+- [Features](#features)
+- [Examples](#examples)
+- [Background and References](#background-and-references)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+To install the ALE Meta-Analysis Package, run:
+
+```bash
+pip install jale
+```
+## Usage
+
+Here’s how to use the project:
+
+JALE requires a project folder that contains 3 files:
+1. Experiment Data (Author, Subjects, Coordinates, Tags)
+2. Analysis Data (Type of ALE, Tags to be included)
+3. Yaml config file (specifying project folder path, filenames and ALE parameters)
+
+For example files please check the docs folder.
+
+Running an ALE can be done in two ways:
+
+1. via CLI: 
+
+```bash
+python -m jale /path/to/yaml/file
+```
+
+2. in Python:
+
+```python
+from jale import main
+
+main(yaml_path='/path/to/yaml/file')
+```
+
+## Features
+
+- Standard ("Main Effect") ALE: Brief description
+- Probabilistic ("Cross-Validated") ALE: Brief description
+- Standard ALE Contrast: Brief description
+- Balanced ALE Contrast: Brief description
+
+## Background and References
+
+This project is based on research by 
+- [Eickhoff et al., 2012](https://doi.org/10.1016/j.neuroimage.2011.09.017).
+- [Eickhoff et al., 2016](https://doi.org/10.1016/j.neuroimage.2016.04.072).
+- [Frahm et al., 2022](https://doi.org/10.1002/hbm.25898).
+- [Frahm et al., 2023](https://doi.org/10.1016/j.neuroimage.2023.120383).

jale-0.1.2/README.md

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+# JALE
+
+A Python package for conducting ALE (Activation Likelihood Estimation) meta-analyses, supporting a range of analysis workflows: standard ALE, probabilistic or cross-validated ALE, standard ALE contrast, and balanced ALE contrast.
+
+## Table of Contents
+- [Installation](#installation)
+- [Usage](#usage)
+- [Features](#features)
+- [Examples](#examples)
+- [Background and References](#background-and-references)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+To install the ALE Meta-Analysis Package, run:
+
+```bash
+pip install jale
+```
+## Usage
+
+Here’s how to use the project:
+
+JALE requires a project folder that contains 3 files:
+1. Experiment Data (Author, Subjects, Coordinates, Tags)
+2. Analysis Data (Type of ALE, Tags to be included)
+3. Yaml config file (specifying project folder path, filenames and ALE parameters)
+
+For example files please check the docs folder.
+
+Running an ALE can be done in two ways:
+
+1. via CLI: 
+
+```bash
+python -m jale /path/to/yaml/file
+```
+
+2. in Python:
+
+```python
+from jale import main
+
+main(yaml_path='/path/to/yaml/file')
+```
+
+## Features
+
+- Standard ("Main Effect") ALE: Brief description
+- Probabilistic ("Cross-Validated") ALE: Brief description
+- Standard ALE Contrast: Brief description
+- Balanced ALE Contrast: Brief description
+
+## Background and References
+
+This project is based on research by 
+- [Eickhoff et al., 2012](https://doi.org/10.1016/j.neuroimage.2011.09.017).
+- [Eickhoff et al., 2016](https://doi.org/10.1016/j.neuroimage.2016.04.072).
+- [Frahm et al., 2022](https://doi.org/10.1002/hbm.25898).
+- [Frahm et al., 2023](https://doi.org/10.1016/j.neuroimage.2023.120383).

jale-0.1.2/jale/__main__.py

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+import sys
+
+from ale import run_ale
+
+
+def cli_ale():
+    if len(sys.argv) == 2:
+        yaml_path = sys.argv[1]
+    else:
+        raise ValueError("No input file provided. Please specify an input file.")
+    run_ale(yaml_path=yaml_path)
+
+
+if __name__ == "__main__":
+    cli_ale()