datamint 2.3.5__py3-none-any.whl → 2.4.0__py3-none-any.whl
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- datamint/api/base_api.py +42 -8
- datamint/api/client.py +2 -0
- datamint/apihandler/base_api_handler.py +0 -1
- datamint/apihandler/dto/annotation_dto.py +2 -0
- datamint/dataset/base_dataset.py +4 -0
- datamint/lightning/__init__.py +1 -0
- datamint/lightning/datamintdatamodule.py +103 -0
- datamint/mlflow/__init__.py +46 -0
- datamint/mlflow/artifact/__init__.py +1 -0
- datamint/mlflow/artifact/datamint_artifacts_repo.py +8 -0
- datamint/mlflow/env_utils.py +109 -0
- datamint/mlflow/env_vars.py +5 -0
- datamint/mlflow/lightning/callbacks/__init__.py +1 -0
- datamint/mlflow/lightning/callbacks/modelcheckpoint.py +338 -0
- datamint/mlflow/models/__init__.py +94 -0
- datamint/mlflow/tracking/datamint_store.py +46 -0
- datamint/mlflow/tracking/default_experiment.py +27 -0
- datamint/mlflow/tracking/fluent.py +78 -0
- datamint-2.4.0.dist-info/METADATA +320 -0
- {datamint-2.3.5.dist-info → datamint-2.4.0.dist-info}/RECORD +22 -9
- datamint-2.4.0.dist-info/entry_points.txt +18 -0
- datamint-2.3.5.dist-info/METADATA +0 -125
- datamint-2.3.5.dist-info/entry_points.txt +0 -4
- {datamint-2.3.5.dist-info → datamint-2.4.0.dist-info}/WHEEL +0 -0
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Metadata-Version: 2.4
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Name: datamint
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Version: 2.4.0
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Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
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Requires-Python: >=3.10
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: 3.14
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Provides-Extra: dev
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Provides-Extra: docs
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Requires-Dist: Deprecated (>=1.2.0)
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Requires-Dist: aioresponses (>=0.7.8,<0.8.0) ; extra == "dev"
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Requires-Dist: albumentations (>=2.0.0)
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Requires-Dist: backports-strenum ; python_version < "3.11"
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Requires-Dist: datamintapi (==0.0.*)
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Requires-Dist: humanize (>=4.0.0,<5.0.0)
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Requires-Dist: lazy-loader (>=0.3.0)
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Requires-Dist: lightning (>=2.0.0,!=2.5.1,!=2.5.1.post0)
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Requires-Dist: matplotlib
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Requires-Dist: medimgkit (>=0.7.3)
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Requires-Dist: mlflow (>=2.0.0,<3.0.0)
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Requires-Dist: sphinx_rtd_theme (>=2.0.0) ; extra == "docs"
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Requires-Dist: torch (>=1.2.0,!=2.3.0)
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Requires-Dist: torchvision (>=0.18.0)
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Description-Content-Type: text/markdown
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# Datamint Python API
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[](https://www.python.org/downloads/)
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A comprehensive Python SDK for interacting with the Datamint platform, providing seamless integration for medical imaging workflows, dataset management, and machine learning experiments.
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## 📋 Table of Contents
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- [Features](#-features)
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- [Installation](#-installation)
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- [Quick Setup](#-quick-setup)
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- [Documentation](#-documentation)
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- [Key Components](#-key-components)
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- [Command Line Tools](#️-command-line-tools)
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- [Examples](#-examples)
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- [Support](#-support)
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## 🚀 Features
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- **Dataset Management**: Download, upload, and manage medical imaging datasets
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- **Annotation Tools**: Create, upload, and manage annotations (segmentations, labels, measurements)
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- **Experiment Tracking**: Integrated MLflow support for experiment management
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- **PyTorch Lightning Integration**: Streamlined ML workflows with Lightning DataModules and callbacks
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- **DICOM Support**: Native handling of DICOM files with anonymization capabilities
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- **Multi-format Support**: PNG, JPEG, NIfTI, and other medical imaging formats
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See the full documentation at https://sonanceai.github.io/datamint-python-api/
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## 📦 Installation
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> [!NOTE]
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> We recommend using a virtual environment to avoid package conflicts.
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### From PyPI
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To be released soon
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### From Source
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```bash
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pip install git+https://github.com/SonanceAI/datamint-python-api
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```
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### Virtual Environment Setup
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<details>
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<summary>Click to expand virtual environment setup instructions</summary>
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We recommend that you install Datamint in a dedicated virtual environment, to avoid conflicting with your system packages.
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For instance, create the enviroment once with `python3 -m venv datamint-env` and then activate it whenever you need it with:
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1. **Create the environment** (one-time setup):
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```bash
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python3 -m venv datamint-env
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```
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2. **Activate the environment** (run whenever you need it):
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| Platform | Command |
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|----------|---------|
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| Linux/macOS | `source datamint-env/bin/activate` |
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| Windows CMD | `datamint-env\Scripts\activate.bat` |
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| Windows PowerShell | `datamint-env\Scripts\Activate.ps1` |
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3. **Install the package**:
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```bash
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pip install git+https://github.com/SonanceAI/datamint-python-api
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```
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</details>
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## Setup API key
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To use the Datamint API, you need to setup your API key (ask your administrator if you don't have one). Use one of the following methods to setup your API key:
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### Method 1: Command-line tool (recommended)
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Run ``datamint-config`` in the terminal and follow the instructions. See [command_line_tools](https://sonanceai.github.io/datamint-python-api/command_line_tools.html) for more details.
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### Method 2: Environment variable
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Specify the API key as an environment variable.
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**Bash:**
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```bash
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export DATAMINT_API_KEY="my_api_key"
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# run your commands (e.g., `datamint-upload`, `python script.py`)
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```
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**Python:**
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```python
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import os
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os.environ["DATAMINT_API_KEY"] = "my_api_key"
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```
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## 📚 Documentation
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| Resource | Description |
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|----------|-------------|
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| [🚀 Getting Started](docs/source/getting_started.rst) | Step-by-step setup and basic usage |
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| [📖 API Reference](docs/source/client_api.rst) | Complete API documentation |
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| [🔥 PyTorch Integration](docs/source/pytorch_integration.rst) | ML workflow integration |
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| [💡 Examples](examples/) | Practical usage examples |
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## 🔗 Key Components
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### Dataset Management
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```python
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from datamint import Dataset
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# Load dataset with annotations
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dataset = Dataset(
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project_name="medical-segmentation",
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)
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# Access data
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for sample in dataset:
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image = sample['image'] # torch.Tensor
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mask = sample['segmentation'] # torch.Tensor (if available)
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metadata = sample['metainfo'] # dict
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```
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### PyTorch Lightning Integration
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```python
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import lightning as L
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from datamint.lightning import DatamintDataModule
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from datamint.mlflow.lightning.callbacks import MLFlowModelCheckpoint
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# Data module
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datamodule = DatamintDataModule(
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project_name="your-project",
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batch_size=16,
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train_split=0.8
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)
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# ML tracking callback
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checkpoint_callback = MLFlowModelCheckpoint(
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monitor="val_loss",
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save_top_k=1,
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register_model_name="best-model"
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)
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# Trainer with MLflow logging
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trainer = L.Trainer(
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max_epochs=100,
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callbacks=[checkpoint_callback],
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logger=L.pytorch.loggers.MLFlowLogger(
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experiment_name="medical-segmentation"
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)
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)
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```
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### Annotation Management
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```python
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# Upload segmentation masks
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api.upload_segmentations(
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resource_id="resource-123",
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file_path="segmentation.nii.gz",
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name="liver_segmentation",
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frame_index=0
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)
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# Add categorical annotations
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api.add_image_category_annotation(
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resource_id="resource-123",
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identifier="diagnosis",
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value="positive"
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)
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# Add geometric annotations
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api.add_line_annotation(
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point1=(10, 20),
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point2=(50, 80),
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resource_id="resource-123",
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identifier="measurement",
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frame_index=5
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)
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```
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## 🛠️ Command Line Tools
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### Upload Resources
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**Upload DICOM files with anonymization:**
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```bash
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datamint-upload \
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--path /path/to/dicoms \
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--recursive \
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--channel "training-data" \
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--anonymize \
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--publish
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```
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**Upload with segmentation masks:**
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```bash
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datamint-upload \
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--path /path/to/images \
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--segmentation_path /path/to/masks \
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--segmentation_names segmentation_config.yaml
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```
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### Configuration Management
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```bash
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# Interactive setup
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datamint-config
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# Set API key
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datamint-config --api-key "your-key"
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```
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## 🔍 Examples
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### Medical Image Segmentation Pipeline
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```python
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import torch
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import lightning as L
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from datamint.lightning import DatamintDataModule
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from datamint.mlflow.lightning.callbacks import MLFlowModelCheckpoint
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class SegmentationModel(L.LightningModule):
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def __init__(self):
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super().__init__()
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# Model definition...
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def training_step(self, batch, batch_idx):
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# Training logic...
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pass
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# Setup data
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datamodule = DatamintDataModule(
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project_name="liver-segmentation",
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batch_size=8,
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train_split=0.8
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)
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# Setup model with MLflow tracking
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model = SegmentationModel()
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checkpoint_cb = MLFlowModelCheckpoint(
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monitor="val_dice",
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mode="max",
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register_model_name="liver-segmentation-model"
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)
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