Metadata-Version: 2.2
Name: openfret
Version: 0.1.3
Summary: A standardized format for single-molecule FRET data
Author-email: "Jieming Li, Leyou Zhang" <jmli@umich.edu>, Leyou Zhang <leyou@umich.edu>
License: MIT License
        
        Copyright (c) [2024] [META-SiM]
        
        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.
Project-URL: Homepage, https://github.com/simol-lab/OpenFRET
Project-URL: Bug Tracker, https://github.com/simol-lab/OpenFRET/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy

# OpenFRET Data Format Python Library

This Python library provides tools for reading and writing single-molecule FRET (Förster Resonance Energy Transfer) data according to the OpenFRET data format specification (version 1.0.0).

## Installation

```bash
pip install openfret
```

## Usage

The library provides classes for representing the different components of the OpenFRET data format: `Dataset`, `Trace`, `Channel`, and `Metadata`.

### Writing Data

```python
from openfret import Dataset, Trace, Channel, Metadata, write_data
from datetime import date

# Create Channel objects
channel1 = Channel("donor", [10.0, 12.0, 15.0], excitation_wavelength=488.0, emission_wavelength=520.0)
channel2 = Channel("acceptor", [2.0, 5.0, 8.0], excitation_wavelength=532.0, emission_wavelength=580.0)

# Create a Trace object
trace1 = Trace([channel1, channel2], metadata=Metadata({"molecule_id": "1"}))

# Create a Dataset object
dataset = Dataset(
    title="My FRET Experiment",
    traces=[trace1],
    description="FRET data of protein folding",
    experiment_type="2-Color FRET",
    authors=["John Doe", "Jane Smith"],
    institution="University X",
    date=date(2024, 1, 1),
    metadata=Metadata({"experiment_id": "20240101_JD_JS_1", "movie_file": "20240101_CoolExperiment.TIF"}),
    sample_details={"buffer_conditions": "Phosphate buffer", "other_details": Metadata({"ph": 7.4})}, #Example of nested metadata
    instrument_details={"microscope": "Olympus IX83", "other_details": Metadata({"objective": "60x oil 1.5 NA"})}, #Example of nested metadata
)

# Write the dataset to a JSON file
write_data(dataset, "fret_data.json", compress=True)
```

### Reading Data

```python
from openfret import read_data

# Read the dataset from a JSON file
loaded_dataset = read_data("fret_data.json.zip")

# Access data
print(loaded_dataset.title)
for trace in loaded_dataset.traces:
    for channel in trace.channels:
        print(f"Channel type: {channel.channel_type}, Data: {channel.data}")
print(loaded_dataset.sample_details["other_details"])
print(loaded_dataset.instrument_details["other_details"])

# Or print the whole dictionary
import json
print(json.dumps(loaded_dataset.to_dict(), indent=4))
```

### Loads traces stored in CSV format
```python
import openfret
root_folder = "fret_data_csv"  # Replace with your root folder path
dataset = openfret.load_csv_traces(root_folder)
openfret.write_data(dataset, "fret_data_from_csv.json", compress=True)
loaded_dataset = openfret.read_data("fret_data_from_csv.json.zip")
print(json.dumps(loaded_dataset.to_dict(), indent=4))
 
 # Example folder structure:
 # fret_data_csv/
 # ├── condition_A/
 # │   ├── trace1.csv
 # │   └── trace2.csv
 # └── condition_B/
 #     ├── trace3.csv
 #     └── trace4.csv
```


## Classes

*   **`Metadata(dict)`:** Represents user-defined metadata. Inherits from `dict` to allow arbitrary key-value pairs.
*   **`Channel`:** Represents a single data channel with intensity data and associated metadata.
    *   `channel_type` (str): String identifier for the channel (e.g., donor, acceptor, FRET).
    *   `excitation_wavelength` (float, optional): Excitation wavelength in nanometers.
    *   `emission_wavelength` (float, optional): Emission wavelength in nanometers.
    *   `exposure_time` (float, optional): Exposure time per frame in seconds.
    *   `data` (List[float]): Intensity values for the channel.
    *   `metadata` (`Metadata`, optional): Metadata for the channel.
*   **`Trace`:** Represents a single-molecule trace containing multiple channels.
    *   `channels` (List[`Channel`]): Array of channel data for this trace.
    *   `metadata` (`Metadata`, optional): Metadata for the trace.
*   **`Dataset`:** Represents a collection of single-molecule traces.
    *   `title` (str): Title of the experiment or dataset.
    *   `description` (str, optional): Detailed description of the experiment.
    *   `experiment_type` (str, optional): Type of experiment.
    *   `authors` (List[str], optional): List of authors.
    *   `institution` (str, optional): Institution where the experiment was conducted.
    *   `date` (`datetime.date`, optional): Date of the experiment.
    *   `traces` (List[`Trace`]): Array of single-molecule traces.
    *   `metadata` (`Metadata`, optional): Metadata for the dataset.
    *   `sample_details` (dict, optional): Details about the sample.
    *   `instrument_details` (dict, optional): Details about the instrument.

## Functions

*   **`write_data(dataset: Dataset, filename: str, compress: bool)`:** Writes a `Dataset` object to a JSON file.
*   **`read_data(filename: str) -> Dataset`:** Reads a `Dataset` object from a JSON file.
*   **`load_csv_traces(root_folder: str) -> Dataset`:** Loads a folder of CSV files into a dataset.

## Contributing

Contributions are welcome! Please open an issue or submit a pull request on GitHub.

## License

MIT License

## Acknowledgements

This library is based on the OpenFRET data format specification.
