torchmil 0.0.1__tar.gz

torchmil-0.0.1/LICENSE

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torchmil-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: torchmil
+Version: 0.0.1
+Summary: Deep Multiple Instance Learning library for Pytorch
+Author-email: Francisco Miguel Castro-Macías <francastro8b@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: homepage, https://franblueee.github.io/torchmil/
+Project-URL: documentation, https://franblueee.github.io/torchmil/api/
+Project-URL: repository, https://github.com/Franblueee/torchmil
+Project-URL: issues, https://github.com/Franblueee/torchmil/issues
+Keywords: deep-learning,pytorch,multiple-instance-learning,multi-instance-learning,mil
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: tensordict
+Requires-Dist: torchmetrics
+Requires-Dist: einops
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: numpy
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+Requires-Dist: mknotebooks; extra == "docs"
+Requires-Dist: mkdocstrings; extra == "docs"
+Requires-Dist: mkdocstrings-python; extra == "docs"
+Requires-Dist: mkdocs-exclude; extra == "docs"
+Provides-Extra: tests
+Requires-Dist: torchmil; extra == "tests"
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pandas; extra == "tests"
+Dynamic: license-file
+
+# torchmil
+
+**torchmil** is a [PyTorch](https://pytorch.org/)-based library for deep Multiple Instance Learning (MIL).
+It provides a simple, flexible, and extensible framework for working with MIL models and data.
+
+It includes:
+
+- A collection of popular [MIL models](https://franblueee.github.io/torchmil/api/models/).
+- Different [PyTorch modules](https://franblueee.github.io/torchmil/api/nn/) frequently used in MIL models.
+- Handy tools to deal with [MIL data](https://franblueee.github.io/torchmil/api/data/).
+- A collection of popular [MIL datasets](https://franblueee.github.io/torchmil/api/datasets/).
+
+## Installation
+
+```bash
+pip install torchmil
+```
+
+## Quick start
+
+You can load a MIL dataset and train a MIL model in just a few lines of code:
+
+```python
+from torchmil.datasets import Camelyon16MIL
+from torchmil.models import ABMIL
+from torchmil.utils import Trainer
+from torchmil.data import collate_fn
+from torch.utils.data import DataLoader
+
+# Load the Camelyon16 dataset
+dataset = Camelyon16MIL(root='data', features='UNI')
+dataloader = DataLoader(dataset, batch_size=4, shuffle=True, collate_fn=collate_fn)
+
+# Instantiate the ABMIL model and optimizer
+model = ABMIL(in_shape=(2048,), criterion=torch.nn.BCEWithLogitsLoss()) # each model has its own criterion
+optimizer = torch.optim.Adam(model.parameters(), lr=1e-4)
+
+# Instantiate the Trainer
+trainer = Trainer(model, optimizer, device='cuda')
+
+# Train the model
+trainer.train(dataloader, epochs=10)
+
+# Save the model
+torch.save(model.state_dict(), 'model.pth')
+```
+
+## Next steps
+
+You can take a look at the [examples](https://franblueee.github.io/torchmil/examples/) to see how to use **torchmil** in practice.
+To see the full list of available models, datasets, and modules, check the [API reference](https://franblueee.github.io/torchmil/api/).
+
+## Citation
+
+If you find this library useful, please consider citing it:
+
+```bibtex
+@misc{torchmil,
+  author = {Castro-Mac{\'\i}as, Francisco M and S{\'a}ez-Maldonado, Francisco Javier and Morales Alvarez, Pablo and Molina, Rafael},
+  title = {torchmil: A PyTorch-based library for deep Multiple Instance Learning},
+  year = {2025},
+  howpublished = {\url{https://franblueee.github.io/torchmil/}}
+}
+```

torchmil-0.0.1/README.md

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+# torchmil
+
+**torchmil** is a [PyTorch](https://pytorch.org/)-based library for deep Multiple Instance Learning (MIL).
+It provides a simple, flexible, and extensible framework for working with MIL models and data.
+
+It includes:
+
+- A collection of popular [MIL models](https://franblueee.github.io/torchmil/api/models/).
+- Different [PyTorch modules](https://franblueee.github.io/torchmil/api/nn/) frequently used in MIL models.
+- Handy tools to deal with [MIL data](https://franblueee.github.io/torchmil/api/data/).
+- A collection of popular [MIL datasets](https://franblueee.github.io/torchmil/api/datasets/).
+
+## Installation
+
+```bash
+pip install torchmil
+```
+
+## Quick start
+
+You can load a MIL dataset and train a MIL model in just a few lines of code:
+
+```python
+from torchmil.datasets import Camelyon16MIL
+from torchmil.models import ABMIL
+from torchmil.utils import Trainer
+from torchmil.data import collate_fn
+from torch.utils.data import DataLoader
+
+# Load the Camelyon16 dataset
+dataset = Camelyon16MIL(root='data', features='UNI')
+dataloader = DataLoader(dataset, batch_size=4, shuffle=True, collate_fn=collate_fn)
+
+# Instantiate the ABMIL model and optimizer
+model = ABMIL(in_shape=(2048,), criterion=torch.nn.BCEWithLogitsLoss()) # each model has its own criterion
+optimizer = torch.optim.Adam(model.parameters(), lr=1e-4)
+
+# Instantiate the Trainer
+trainer = Trainer(model, optimizer, device='cuda')
+
+# Train the model
+trainer.train(dataloader, epochs=10)
+
+# Save the model
+torch.save(model.state_dict(), 'model.pth')
+```
+
+## Next steps
+
+You can take a look at the [examples](https://franblueee.github.io/torchmil/examples/) to see how to use **torchmil** in practice.
+To see the full list of available models, datasets, and modules, check the [API reference](https://franblueee.github.io/torchmil/api/).
+
+## Citation
+
+If you find this library useful, please consider citing it:
+
+```bibtex
+@misc{torchmil,
+  author = {Castro-Mac{\'\i}as, Francisco M and S{\'a}ez-Maldonado, Francisco Javier and Morales Alvarez, Pablo and Molina, Rafael},
+  title = {torchmil: A PyTorch-based library for deep Multiple Instance Learning},
+  year = {2025},
+  howpublished = {\url{https://franblueee.github.io/torchmil/}}
+}
+```

torchmil-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "torchmil"
+version = "0.0.1"
+authors = [
+    { name="Francisco Miguel Castro-Macías", email="francastro8b@gmail.com" },
+]
+description = "Deep Multiple Instance Learning library for Pytorch"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "Apache-2.0"
+keywords=[
+    "deep-learning",
+    "pytorch",
+    "multiple-instance-learning",
+    "multi-instance-learning",
+    "mil",
+]
+classifiers = [
+    "Intended Audience :: Developers",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Mathematics",
+]
+dependencies = [
+    "torch",
+    "tensordict",
+    "torchmetrics",
+    "einops",
+    "scipy",
+    "tqdm",
+    "numpy",
+]
+
+[project.optional-dependencies]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mknotebooks",
+    "mkdocstrings",
+    "mkdocstrings-python",
+    "mkdocs-exclude",
+]
+tests = [
+    "torchmil",
+    "pytest",
+    "pytest-cov",
+    "pandas",
+]
+
+[project.urls]
+homepage = "https://franblueee.github.io/torchmil/"
+documentation = "https://franblueee.github.io/torchmil/api/"
+repository = "https://github.com/Franblueee/torchmil"
+issues = "https://github.com/Franblueee/torchmil/issues"
+
+[tool.flake8]
+max-line-length = 100
+exclude = [".ipynb", "build", ".pytest_cache"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.setuptools.packages.find]
+where = ["."]

torchmil-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

torchmil-0.0.1/tests/data/test_collate.py

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+import pytest
+import torch
+from torchmil.data.collate import pad_tensors, collate_fn
+from tensordict import TensorDict
+
+def test_pad_tensors_single_tensor():
+    # Test the pad_tensors function with a single tensor.
+    # Ensure that the tensor is padded correctly and the mask is generated as expected.
+    tensor = torch.tensor([[1, 2], [3, 4]])
+    padded_tensor, mask = pad_tensors([tensor], padding_value=0)
+
+    assert padded_tensor.shape == (1, 2, 2)
+    assert torch.equal(padded_tensor[0], tensor)
+    assert torch.equal(mask, torch.tensor([[1, 1]], dtype=torch.uint8))
+
+def test_pad_tensors_multiple_tensors():
+    # Test the pad_tensors function with multiple tensors of varying sizes.
+    # Verify that all tensors are padded to the same size and the mask is correct.
+    tensor1 = torch.tensor([[1, 2], [3, 4]])
+    tensor2 = torch.tensor([[5, 6]])
+    padded_tensor, mask = pad_tensors([tensor1, tensor2], padding_value=0)
+
+    assert padded_tensor.shape == (2, 2, 2)
+    assert torch.equal(padded_tensor[0], tensor1)
+    assert torch.equal(padded_tensor[1], torch.tensor([[5, 6], [0, 0]]))
+    assert torch.equal(mask, torch.tensor([[1, 1], [1, 0]], dtype=torch.uint8))
+
+def test_collate_fn_dense_tensors():
+    # Test the collate_fn function with dense tensors.
+    # Check that the tensors are collated correctly into a TensorDict with proper padding and masks.
+    batch_list = [
+        {"data": torch.tensor([[1, 2], [3, 4]])},
+        {"data": torch.tensor([[5, 6]])}
+    ]
+    result = collate_fn(batch_list, sparse=False)
+
+    assert isinstance(result, TensorDict)
+    assert "data" in result
+    assert "mask" in result
+    assert result["data"].shape == (2, 2, 2)
+    assert torch.equal(result["data"][0], torch.tensor([[1, 2], [3, 4]]))
+    assert torch.equal(result["data"][1], torch.tensor([[5, 6], [0, 0]]))
+    assert torch.equal(result["mask"], torch.tensor([[1, 1], [1, 0]], dtype=torch.uint8))
+
+def test_collate_fn_sparse_tensors():
+    # Test the collate_fn function with sparse tensors.
+    # Ensure that sparse tensors are collated correctly into a TensorDict.
+    sparse_tensor1 = torch.sparse_coo_tensor(
+        indices=[[0, 1], [0, 1]],
+        values=[1, 2],
+        size=(2, 2)
+    )
+    sparse_tensor2 = torch.sparse_coo_tensor(
+        indices=[[0], [0]],
+        values=[3],
+        size=(2, 2)
+    )
+    batch_list = [
+        {"data": sparse_tensor1},
+        {"data": sparse_tensor2}
+    ]
+    result = collate_fn(batch_list, sparse=True)
+
+    assert isinstance(result, TensorDict)
+    assert "data" in result
+    assert result["data"].is_sparse
+    assert result["data"].shape == (2, 2, 2)