datamint 2.3.3__py3-none-any.whl → 2.9.0__py3-none-any.whl

datamint/mlflow/tracking/fluent.py

@@ -0,0 +1,91 @@
+from typing import TYPE_CHECKING
+import threading
+import logging
+from datamint import Api
+from datamint.exceptions import DatamintException
+import os
+from datamint.mlflow.env_vars import EnvVars
+from datamint.mlflow.env_utils import ensure_mlflow_configured
+
+if TYPE_CHECKING:
+    from datamint.entities.project import Project
+
+_PROJECT_LOCK = threading.Lock()
+_LOGGER = logging.getLogger(__name__)
+
+_ACTIVE_PROJECT_ID: str | None = None
+
+
+def get_active_project_id() -> str | None:
+    """
+    Get the active project ID from the environment variable or the global variable.
+    """
+    global _ACTIVE_PROJECT_ID
+
+    if _ACTIVE_PROJECT_ID is not None:
+        return _ACTIVE_PROJECT_ID
+    # Check if the environment variable is set
+    project_id = os.getenv(EnvVars.DATAMINT_PROJECT_ID.value)
+    if project_id is not None:
+        _ACTIVE_PROJECT_ID = project_id
+        return project_id
+    project_name = os.getenv(EnvVars.DATAMINT_PROJECT_NAME.value)
+    if project_name is not None:
+        project = _find_project_by_name(project_name)
+        if project is not None:
+            _ACTIVE_PROJECT_ID = project['id']
+            return _ACTIVE_PROJECT_ID
+
+    return None
+
+
+def _find_project_by_name(project_name: str):
+    dt_client = Api(check_connection=False)
+    project = dt_client.projects.get_by_name(project_name)
+    if project is None:
+        raise DatamintException(f"Project with name '{project_name}' does not exist.")
+    return project
+
+
+def _get_project_by_name_or_id(project_name_or_id: str) -> 'Project':
+    dt_client = Api(check_connection=False)
+    # If length >= 32, likely an ID
+    if len(project_name_or_id) >= 32 and ' ' not in project_name_or_id:
+        # Try to get by ID first
+        project = dt_client.projects.get_by_id(project_name_or_id)
+        if project is not None:
+            return project
+    project = dt_client.projects.get_by_name(project_name_or_id)
+    if project is None:
+        raise DatamintException(f"Project '{project_name_or_id}' does not exist.")
+    return project
+
+
+def set_project(project: 'Project | str'):
+    """
+    Set the active project for the current session.
+    
+    Args:
+        project: The Project instance or project name/ID to set as active.
+    """
+    global _ACTIVE_PROJECT_ID
+
+    # Ensure MLflow is properly configured before proceeding
+    ensure_mlflow_configured()
+
+    with _PROJECT_LOCK:
+        if isinstance(project, str):
+            project_id = None
+            project = _get_project_by_name_or_id(project)
+            project_id = project.id
+        else:
+            # It's a Project entity
+            project_id = project.id
+
+        _ACTIVE_PROJECT_ID = project_id
+
+    # Set 'DATAMINT_PROJECT_ID' environment variable
+    # so that subprocess can inherit it.
+    os.environ[EnvVars.DATAMINT_PROJECT_ID.value] = project_id
+
+    return project

datamint/utils/env.py

@@ -0,0 +1,27 @@
+def is_jupyter_env():
+    """Check if code is running in a Jupyter notebook environment."""
+    try:
+        # Check for IPython kernel
+        from IPython import get_ipython
+        if get_ipython() is None:
+            return False
+
+        # Check if it's specifically a notebook (not just IPython terminal)
+        if 'IPKernelApp' in get_ipython().config:
+            return True
+    except (ImportError, AttributeError):
+        pass
+
+    return False
+
+
+_ASYNCIO_LOOP_PATCHED = False
+
+
+def ensure_asyncio_loop():
+    """Ensure that the asyncio event loop is properly set up for Jupyter notebooks."""
+    global _ASYNCIO_LOOP_PATCHED
+    if not _ASYNCIO_LOOP_PATCHED and is_jupyter_env():
+        import nest_asyncio
+        nest_asyncio.apply()
+        _ASYNCIO_LOOP_PATCHED = True

datamint/utils/visualization.py

@@ -5,23 +5,26 @@ from torch import Tensor
 import torchvision.utils
 import torch
 import colorsys
+from collections.abc import Sequence
 
 
-def show(imgs: list[Tensor] | Tensor,
-         figsize: tuple[int, int] = None,
+def show(imgs: Sequence[Tensor | np.ndarray] | Tensor | np.ndarray,
+         figsize: tuple[int, int] | None = None,
          normalize: bool = False):
     """
     Show a list of images in a grid.
     Args:
-        imgs (list[Tensor] | Tensor): List of images to show.
+        imgs (Sequence[Tensor | np.ndarray] | Tensor | np.ndarray): List of images to show.
             Each image should be a tensor of shape (C, H, W) and dtype uint8 or float.
         figsize (tuple[int, int], optional): Size of the figure. Defaults to None.
         normalize (bool, optional): Whether to normalize the images to [0, 1] range by min-max scaling.
     """
 
-    if not isinstance(imgs, list):
+    if not isinstance(imgs, list) and not isinstance(imgs, tuple):
         imgs = [imgs]
 
+    imgs = [img if isinstance(img, torch.Tensor) else torch.from_numpy(img) for img in imgs]
+
     if normalize:
         for i, img in enumerate(imgs):
             img = img.float()
@@ -72,10 +75,10 @@ def generate_color_palette(num_objects: int) -> list[tuple[int, int, int]]:
     return colors
 
 
-@torch.no_grad()
+@torch.inference_mode()
 def draw_masks(
-    image: Tensor,
-    masks: Tensor,
+    image: Tensor | np.ndarray,
+    masks: Tensor | np.ndarray,
     alpha: float = 0.5,
     colors: list[str | tuple[int, int, int]] | str | tuple[int, int, int] | None = None,
 ) -> Tensor:
@@ -85,7 +88,7 @@ def draw_masks(
     The image values should be uint8 or float.
 
     Args:
-        image (Tensor): Tensor of shape (3, H, W) and dtype uint8 or float.
+        image (Tensor): Tensor of shape (3, H, W) or (H, W) and dtype uint8 or float.
         masks (Tensor): Tensor of shape (num_masks, H, W) or (H, W) and dtype bool.
         alpha (float): Float number between 0 and 1 denoting the transparency of the masks.
             0 means full transparency, 1 means no transparency.
@@ -97,11 +100,19 @@ def draw_masks(
     Returns:
         img (Tensor[C, H, W]): Image Tensor, with segmentation masks drawn on top.
     """
-    
+
+    if isinstance(image, np.ndarray):
+        image = torch.from_numpy(image)
+
+    if isinstance(masks, np.ndarray):
+        masks = torch.from_numpy(masks)
 
     if image.ndim == 3 and image.shape[0] == 1:
         # convert to RGB
         image = image.expand(3, -1, -1)
+    if image.ndim == 2:
+        # convert to RGB
+        image = image.unsqueeze(0).expand(3, -1, -1)
 
     if masks.dtype != torch.bool:
         masks = masks.bool()
@@ -113,10 +124,7 @@ def draw_masks(
         image = image / image.max()
 
     if masks.ndim == 2:
-        return torchvision.utils.draw_segmentation_masks(image=image,
-                                                         masks=masks,
-                                                         alpha=alpha,
-                                                         colors=colors)
+        masks = masks.unsqueeze(0)
 
     if colors is None:
         colors = generate_color_palette(len(masks))

datamint-2.9.0.dist-info/METADATA

@@ -0,0 +1,220 @@
+Metadata-Version: 2.4
+Name: datamint
+Version: 2.9.0
+Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
+Requires-Python: >=3.10
+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 :: 3.14
+Provides-Extra: dev
+Provides-Extra: docs
+Requires-Dist: Deprecated (>=1.2.0)
+Requires-Dist: aiohttp (>=3.0.0,<4.0.0)
+Requires-Dist: aioresponses (>=0.7.8,<0.8.0) ; extra == "dev"
+Requires-Dist: albumentations (>=2.0.0)
+Requires-Dist: backports-strenum ; python_version < "3.11"
+Requires-Dist: certifi (>=2025.0.0)
+Requires-Dist: httpx
+Requires-Dist: humanize (>=4.0.0,<5.0.0)
+Requires-Dist: lazy-loader (>=0.3.0)
+Requires-Dist: lightning[extra] (>=2.0.0,!=2.5.1,!=2.5.1.post0)
+Requires-Dist: matplotlib
+Requires-Dist: medimgkit (>=0.11.2)
+Requires-Dist: mlflow (>=3.8.1)
+Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
+Requires-Dist: nibabel (>=4.0.0)
+Requires-Dist: numpy
+Requires-Dist: opencv-python (>=4.0.0)
+Requires-Dist: pandas (>=2.0.0)
+Requires-Dist: platformdirs (>=4.0.0,<5.0.0)
+Requires-Dist: pydantic (>=2.6.4)
+Requires-Dist: pydicom (>=3.0.0,<4.0.0)
+Requires-Dist: pylibjpeg (>=2.0.0,<3.0.0)
+Requires-Dist: pylibjpeg-libjpeg (>=2.0.0,<3.0.0)
+Requires-Dist: pytest (>=7.0.0,<8.0.0) ; extra == "dev"
+Requires-Dist: pytest-cov (>=4.0.0,<5.0.0) ; extra == "dev"
+Requires-Dist: pyyaml (>=5.0.0)
+Requires-Dist: requests (>=2.0.0,<3.0.0)
+Requires-Dist: responses (>=0.20.0,<0.21.0) ; extra == "dev"
+Requires-Dist: respx (>=0.22.0) ; extra == "dev"
+Requires-Dist: rich (>=10.0.0)
+Requires-Dist: setuptools (>=57.0) ; extra == "docs"
+Requires-Dist: sphinx (>=5.0) ; extra == "docs"
+Requires-Dist: sphinx-tabs (>=3.0.0) ; extra == "docs"
+Requires-Dist: sphinx_rtd_theme (>=2.0.0) ; extra == "docs"
+Requires-Dist: torch (>=1.2.0,!=2.3.0)
+Requires-Dist: torchvision (>=0.18.0)
+Requires-Dist: tqdm (>=4.0.0,<5.0.0)
+Requires-Dist: typing_extensions (>=4.0.0)
+Description-Content-Type: text/markdown
+
+# Datamint Python API
+
+![Build Status](https://github.com/SonanceAI/datamint-python-api/actions/workflows/run_test.yaml/badge.svg)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A comprehensive Python SDK for interacting with the Datamint platform, providing seamless integration for medical imaging workflows, dataset management, and machine learning experiments.
+
+## 📋 Table of Contents
+
+- [Features](#-features)
+- [Installation](#-installation)
+- [Quick Setup](#-setup-api-key)
+- [Documentation](#-documentation)
+- [Command Line Tools](#️-command-line-tools)
+- [Support](#-support)
+
+## 🚀 Features
+
+- **Dataset Management**: Download, upload, and manage medical imaging datasets
+- **Annotation Tools**: Create, upload, and manage annotations (segmentations, labels, measurements)
+- **Experiment Tracking**: Integrated MLflow support for experiment management
+- **PyTorch Lightning Integration**: Streamlined ML workflows with Lightning DataModules and callbacks
+- **DICOM Support**: Native handling of DICOM files with anonymization capabilities
+- **Multi-format Support**: PNG, JPEG, NIfTI, and other medical imaging formats
+
+See the full documentation at https://sonanceai.github.io/datamint-python-api/
+
+## 📦 Installation
+
+> [!NOTE]
+> We recommend using a virtual environment to avoid package conflicts.
+
+### From PyPI
+
+`pip install -U datamint`
+
+### Virtual Environment Setup
+
+<details>
+<summary>Click to expand virtual environment setup instructions</summary>
+
+We recommend that you install Datamint in a dedicated virtual environment, to avoid conflicting with your system packages.
+For instance, create the enviroment once with `python3 -m venv datamint-env` and then activate it whenever you need it with:
+
+1. **Create the environment** (one-time setup):
+   ```bash
+   python3 -m venv datamint-env
+   ```
+
+2. **Activate the environment** (run whenever you need it):
+   
+   | Platform | Command |
+   |----------|---------|
+   | Linux/macOS | `source datamint-env/bin/activate` |
+   | Windows CMD | `datamint-env\Scripts\activate.bat` |
+   | Windows PowerShell | `datamint-env\Scripts\Activate.ps1` |
+
+3. **Install the package**:
+   ```bash
+   pip install datamint
+   ```
+
+</details>
+
+## ⚙ Setup API key
+
+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:
+
+### Method 1: Command-line tool (recommended)
+
+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#configuring-the-datamint-settings) for more details.
+
+### Method 2: Environment variable
+
+Specify the API key as an environment variable.
+
+**Bash:**
+```bash
+export DATAMINT_API_KEY="my_api_key"
+# run your commands (e.g., `datamint-upload`, `python script.py`)
+```
+
+**Python:**
+```python
+import os
+os.environ["DATAMINT_API_KEY"] = "my_api_key"
+```
+
+## 📚 Documentation
+
+| Resource | Description |
+|----------|-------------|
+| [🚀 Getting Started](https://sonanceai.github.io/datamint-python-api/getting_started.html) | Step-by-step setup and basic usage |
+| [📖 API Reference](https://sonanceai.github.io/datamint-python-api/client_api.html) | Complete API documentation |
+| [🔥 PyTorch Integration](https://sonanceai.github.io/datamint-python-api/pytorch_integration.html) | ML workflow integration |
+| [💡 Examples](examples/) | Practical usage examples |
+
+## 🛠️ Command Line Tools
+
+Full documentation at [command_line_tools](https://sonanceai.github.io/datamint-python-api/command_line_tools.html).
+
+### Upload Resources
+
+**Upload DICOM files with anonymization:**
+```bash
+datamint-upload /path/to/dicoms --recursive --channel "training-data" --publish --tag "my_data_tag"
+```
+It anonymizes by default.
+
+### Configuration Management
+
+```bash
+# Interactive setup
+datamint-config
+
+# Set API key
+datamint-config --api-key "your-key"
+```
+
+## 🔒 SSL Certificate Troubleshooting
+
+If you encounter SSL certificate verification errors like:
+```
+SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate
+```
+
+### Quick Fix
+
+**1. Upgrade certifi:**
+```bash
+pip install --upgrade certifi
+```
+
+**2. Set environment variables:**
+```bash
+export SSL_CERT_FILE=$(python -m certifi)
+export REQUESTS_CA_BUNDLE=$(python -m certifi)
+```
+
+**3. Run your script:**
+```bash
+python your_script.py
+```
+
+### Alternative Solutions
+
+**Option 1: Use Custom CA Bundle**
+```python
+from datamint import Api
+
+api = Api(verify_ssl="/path/to/your/ca-bundle.crt")
+```
+
+**Option 2: Disable SSL Verification (Development Only)**
+```python
+from datamint import Api
+
+# ⚠️ WARNING: Only use in development with self-signed certificates
+api = Api(verify_ssl=False)
+```
+
+## 🆘 Support
+
+[Full Documentation](https://datamint-python-api.readthedocs.io/)  
+[GitHub Issues](https://github.com/SonanceAI/datamint-python-api/issues)
+
+

datamint-2.9.0.dist-info/RECORD

@@ -0,0 +1,73 @@
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+datamint/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+datamint/api/base_api.py,sha256=EijBpBDJbwJ4MkWPN1ZnKz5SR-QxB2gq4FKj4HOAr7c,28584
+datamint/api/client.py,sha256=o9BQUe7iYJGUn6rNjRg6vv_SlIUXYVU8N0YpRNFznFw,6455
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+datamint/lightning/__init__.py,sha256=8Od8e-nWi4pNn1m5CQsIV8ElitVEUoHxEBiT2GVfJUc,50
+datamint/lightning/datamintdatamodule.py,sha256=yTch-H0QCAQh_lwls8sCfofKqP0nPssy0CpSsO8QeEI,4038
+datamint/logging.yaml,sha256=tOMxtc2UmwlIMTK6ljtnBwTco1PNrPeq3mx2iMuSbiw,482
+datamint/mlflow/__init__.py,sha256=vQP9MR_1Nf_A4L_rdBCNPD7Oaj9Cxj2GVMQ-eCfmnEA,2427
+datamint/mlflow/artifact/__init__.py,sha256=XwZ4u63VoB9EdAx3mTwoOp-2PmMfa7KPBVPV0kZFUh0,64
+datamint/mlflow/artifact/datamint_artifacts_repo.py,sha256=e97U4SF1bq8j_OTiZofuY92eIdgBuw9J8cyhW72ez6A,353
+datamint/mlflow/env_utils.py,sha256=Q9STQdFyk1f1Lkf3ZvU6xf0EcPoivx2dPDBeVdgwT5Q,4815
+datamint/mlflow/env_vars.py,sha256=H3iteY7o_Jj3_EU9vREBE4s62SZMmiO6-ubC5_xG2kU,144
+datamint/mlflow/flavors/__init__.py,sha256=GTJqHZT_TiNirIOto-42AMKKbXXyChQQdoLpMh6t_fE,274
+datamint/mlflow/flavors/datamint_flavor.py,sha256=Y6BMAJ4neltz1SiL-uxgM5FUePEwAAMpDiH8RmTpc18,5335
+datamint/mlflow/flavors/model.py,sha256=4kaz9C4KZV1ZDcrhFzvn89Pw8Aq_sN_pxyBsbL-O01o,33511
+datamint/mlflow/lightning/callbacks/__init__.py,sha256=4Y-54OFIKBiwD_AwbWr2JRNyWBYsz9vnagfZfKgdKA0,50
+datamint/mlflow/lightning/callbacks/modelcheckpoint.py,sha256=Lry9RR8HJM6NOw_vPJ7RG7VLUI6WGa9NzBO1Z77bRZc,18124
+datamint/mlflow/models/__init__.py,sha256=LgTImfBg3OY8cWCzQw1Af_e9VY0IOIj66BQ8sY_U3TI,3608
+datamint/mlflow/tracking/datamint_store.py,sha256=h24dtseWJlJFYiOYkXP2JaT_XAOand3a8KNcAq33wkQ,3180
+datamint/mlflow/tracking/default_experiment.py,sha256=gzrIZng0DpI2GWa8X30JVAq2fteq4w8cg4nz3UxYCvc,934
+datamint/mlflow/tracking/fluent.py,sha256=brvShypy167sbJ8mAtu5prASDFeOAsXkO6Fm85PmjPM,2852
+datamint/types.py,sha256=2OaY5QJvQIJKxyMNJYzxBksKCa9ZS2gb_ayJrByvu2Y,410
+datamint/utils/env.py,sha256=lItXhaAKto6hB33yZ9369fxolrobeZSGXI3-L3_WoqA,789
+datamint/utils/logging_utils.py,sha256=9pRoaPrWu2jOdDCiAoUsjEdP5ZwaealWL3hjUqFvx9g,4022
+datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
+datamint/utils/visualization.py,sha256=6xmVbKIkpcyOf_f0lmv_GG8JrrWZe7s_YzP_YC8H1MU,4751
+datamint-2.9.0.dist-info/METADATA,sha256=hMQPkCTwu_SO_J275fMlpmXCzdeT7Zt8JCMHH9qmZ40,7249
+datamint-2.9.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+datamint-2.9.0.dist-info/entry_points.txt,sha256=wTr9DXteCfAFqLUstN1Qx_SqC_rFLrAUIcDx9q1eXZw,845
+datamint-2.9.0.dist-info/RECORD,,

{datamint-2.3.3.dist-info → datamint-2.9.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any

datamint-2.9.0.dist-info/entry_points.txt

@@ -0,0 +1,18 @@
+[console_scripts]
+datamint-config=datamint.client_cmd_tools.datamint_config:main
+datamint-upload=datamint.client_cmd_tools.datamint_upload:main
+
+[mlflow.artifact_repository]
+datamint=datamint.mlflow.artifact.datamint_artifacts_repo:DatamintArtifactsRepository
+http=datamint.mlflow.artifact.datamint_artifacts_repo:DatamintArtifactsRepository
+https=datamint.mlflow.artifact.datamint_artifacts_repo:DatamintArtifactsRepository
+mlflow-artifacts=datamint.mlflow.artifact.datamint_artifacts_repo:DatamintArtifactsRepository
+
+[mlflow.default_experiment_provider]
+datamint=datamint.mlflow.tracking.default_experiment:DatamintExperimentProvider
+
+[mlflow.tracking_store]
+datamint=datamint.mlflow.tracking.datamint_store:DatamintStore
+http=datamint.mlflow.tracking.datamint_store:DatamintStore
+https=datamint.mlflow.tracking.datamint_store:DatamintStore
+