Add README

Author: tstoeter

README.md

@@ -0,0 +1,114 @@
+# Datenbiene
+
+**Datenbiene** (data bee) is a versatile and powerful data collection tool
+designed for multi-modal scientific studies. It facilitates the collection of
+data from multiple modalities on different acquisition systems, offering
+flexibility and efficiency in managing research data directly after acquisition.
+
+
+## Features
+
+* Collects data from various sources and modalities / acquisition devices.
+* Provides easy configuration through Excel and JSON files.
+* Utilizes Jinja2 templates for dynamic placeholders in Excel cells.
+* Extensible with custom sources, sinks, and checkers.
+
+
+## Installation
+
+Ensure you have Python 3 installed. You can install the required packages using
+the `requirements.txt` file in a virtual environment:
+
+1. Create a Python virtual environment and activate it:
+
+    ```sh
+    python -m venv env
+    source env/bin/activate  # On Windows use `env\Scripts\activate`
+    ```
+
+2. Install the dependencies using pip:
+
+    ```sh
+    pip install -r requirements.txt
+    ```
+
+3. Modify settings and secrets in `config.py` according to your setup.
+
+
+## Usage
+
+To use Datenbiene, you need to provide an Excel file containing the
+configuration for sources, checkers, and sinks, along with an optional JSON file
+for key-value pairs.
+
+### Command-line Arguments
+
+* `-e, --excel`: Path to the Excel file containing Sources and Sinks sheets. (required)
+* `-j, --json`: Path to the JSON file containing key-value pairs. (required)
+
+### Example
+
+```sh
+python datenbiene.py -e sources-sinks.xlsx -j key-vals.json
+```
+
+
+## Configuration
+
+The configuration Excel file should contain the following sheets:
+
+- Sources: Specifies the data sources.
+- Checkers: Defines data checkers (to be implemented).
+- Sinks: Specifies the data sinks.
+
+The JSON file should contain key-value pairs used for dynamic data processing
+with Jinja2 templates applied to all cells in the Excel file.
+
+### Example Excel File
+
+| Name   | Source     | PathPatterns  | FilePatterns | AdditionalOptions |
+|--------|------------|---------------|--------------|-------------------|
+| Source | SomeSource | /path/to/data | *.csv        | {"option1": "value1"} |
+
+### Example JSON File
+
+```json
+{
+  "study": "multi-modal-study-01",
+  "subject": "ab12",
+  "date": 20250202
+}
+```
+
+
+## Customization
+
+You can extend Datenbiene by adding custom sources, sinks, and checkers.
+Implement your custom classes in the `sources`, `sinks`, and `checkers` modules,
+respectively, and update the Excel configuration accordingly.
+
+
+## License
+
+Datenbiene is licensed under the GPL-3.0-only license. See LICENSE file or
+https://www.gnu.org/licenses/gpl-3.0.html for details.
+
+
+## Authors
+
+Datenbiene is developed by
+
+* Torsten Stöter ([email protected])
+* Jörg Stadler
+* André Brechmann
+
+all affiliated with Combinatorial NeuroImaging Core Facility at Leibniz
+Institute for Neurobiology Magdeburg, Germany.
+
+
+## Acknowledgements
+
+A special thank you goes to our colleagues Andreas Fügner, Anke Michalsky and
+Renate Blobel-Lüer for their continued support in testing and valuable feedback
+for improving the Datenbiene software.
+