pyg-nightly 2.7.0.dev20250521__py3-none-any.whl → 2.7.0.dev20250523__py3-none-any.whl

{pyg_nightly-2.7.0.dev20250521.dist-info → pyg_nightly-2.7.0.dev20250523.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250521
+Version: 2.7.0.dev20250523
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>

{pyg_nightly-2.7.0.dev20250521.dist-info → pyg_nightly-2.7.0.dev20250523.dist-info}/RECORD

@@ -1,4 +1,4 @@
-torch_geometric/__init__.py,sha256=ABRQ7cUyuHSYpjKfHb96NZXDfgWhxwlkTdCh2eOTTA8,2255
+torch_geometric/__init__.py,sha256=NXgdZz24rbtahQqr0QfFVgXBwIpbaGoTZSu_4JTmXd8,2255
 torch_geometric/_compile.py,sha256=f-WQeH4VLi5Hn9lrgztFUCSrN_FImjhQa6BxFzcYC38,1338
 torch_geometric/_onnx.py,sha256=V9ffrIKSqhDw6xUZ12lkuSfNs48cQp2EeJ6Z19GfnVw,349
 torch_geometric/backend.py,sha256=lVaf7aLoVaB3M-UcByUJ1G4T4FOK6LXAg0CF4W3E8jo,1575
@@ -55,7 +55,7 @@ torch_geometric/data/temporal.py,sha256=WOJ6gFrTLikaLhUvotyUF5ql14FkE5Ox3hNkdSp6
 torch_geometric/data/view.py,sha256=XjkVSc-UWZFCT4DlXLShZtO8duhFQkS9gq88zZXANsk,1089
 torch_geometric/data/lightning/__init__.py,sha256=w3En1tJfy3kSqe1MycpOyZpHFO3fxBCgNCUOznPA3YU,178
 torch_geometric/data/lightning/datamodule.py,sha256=Bn9iaIfE4NWDDWWMqCvBeZ4bIW1Silx_Ol5CPJCliaQ,29242
-torch_geometric/datasets/__init__.py,sha256=fgJgc2wztjTJKczuHwXH7L0CgCXw69o_Dtm1KnleMCY,6235
+torch_geometric/datasets/__init__.py,sha256=vIraHnDqD40Num-XwwNivjHQDboK9tmMvlZHjTAuljM,6291
 torch_geometric/datasets/actor.py,sha256=oUxgJIX8bi5hJr1etWNYIFyVQNDDXi1nyVpHGGMEAGQ,4304
 torch_geometric/datasets/airfrans.py,sha256=212gYsk7PvF-qcmvM2YXaOBhFrS79evAGg_sPHXih4w,5439
 torch_geometric/datasets/airports.py,sha256=b3gkv3gY2JkUpmGiz36Z-g7EcnSfU8lBG1YsCOWdJ6k,3758
@@ -115,6 +115,7 @@ torch_geometric/datasets/linkx_dataset.py,sha256=_DsF5d2-o79-WibEKojIJKCpCF3VVxS
 torch_geometric/datasets/lrgb.py,sha256=lOlzYCn9XbwQb3HK_wdufqjqK_aZbnoUqZu0NXZ6Oyw,11657
 torch_geometric/datasets/malnet_tiny.py,sha256=E_ymC7_XS8rgZelcdevZyCDVjX5Ov21G6vwrG0JgAP0,5271
 torch_geometric/datasets/md17.py,sha256=Wv-Q75uUDrFjRur5nOvg2TSw68UxkdYDJvkf3YA-T70,16735
+torch_geometric/datasets/medshapenet.py,sha256=eCBCXKpueweCwDSf_Q4_MwVA3IbJd04FSxnknLnMHTk,5567
 torch_geometric/datasets/mixhop_synthetic_dataset.py,sha256=4NNvTHUvvV6pcqQCyVDS5XhppXUeF2H9GTfFoc49eyU,3951
 torch_geometric/datasets/mnist_superpixels.py,sha256=o2ArbZ0_OE0u8VCaHmWwvngESlOFr9oM9dSEP_tjAS4,3340
 torch_geometric/datasets/modelnet.py,sha256=-qmLjlQiKVWmtHefAIIE97dQxEcaBfetMJnvgYZuwkg,5347
@@ -637,7 +638,7 @@ torch_geometric/utils/undirected.py,sha256=H_nfpI0_WluOG6VfjPyldvcjL4w5USAKWu2x5
 torch_geometric/visualization/__init__.py,sha256=b-HnVesXjyJ_L1N-DnjiRiRVf7lhwKaBQF_2i5YMVSU,208
 torch_geometric/visualization/graph.py,sha256=mfZHXYfiU-CWMtfawYc80IxVwVmtK9hbIkSKhM_j7oI,14311
 torch_geometric/visualization/influence.py,sha256=CWMvuNA_Nf1sfbJmQgn58yS4OFpeKXeZPe7kEuvkUBw,477
-pyg_nightly-2.7.0.dev20250521.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
-pyg_nightly-2.7.0.dev20250521.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-pyg_nightly-2.7.0.dev20250521.dist-info/METADATA,sha256=TBjJORONYN_qTyeZPxfKdnHp84pDrSXqyQcWqPEi03M,62952
-pyg_nightly-2.7.0.dev20250521.dist-info/RECORD,,
+pyg_nightly-2.7.0.dev20250523.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
+pyg_nightly-2.7.0.dev20250523.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+pyg_nightly-2.7.0.dev20250523.dist-info/METADATA,sha256=XmGjWnQyn7JYMg0nbBui3cBtMAOzlbVqR-Q5iXFK-I4,62952
+pyg_nightly-2.7.0.dev20250523.dist-info/RECORD,,

torch_geometric/__init__.py

@@ -31,7 +31,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250521'
+__version__ = '2.7.0.dev20250523'
 
 __all__ = [
     'Index',

torch_geometric/datasets/__init__.py

@@ -30,6 +30,7 @@ from .faust import FAUST
 from .dynamic_faust import DynamicFAUST
 from .shapenet import ShapeNet
 from .modelnet import ModelNet
+from .medshapenet import MedShapeNet
 from .coma import CoMA
 from .shrec2016 import SHREC2016
 from .tosca import TOSCA
@@ -147,6 +148,7 @@ homo_datasets = [
     'DynamicFAUST',
     'ShapeNet',
     'ModelNet',
+    'MedShapeNet',
     'CoMA',
     'SHREC2016',
     'TOSCA',

torch_geometric/datasets/medshapenet.py

@@ -0,0 +1,144 @@
+import os
+import os.path as osp
+from typing import Callable, List, Optional
+
+import numpy as np
+import torch
+
+from torch_geometric.data import Data, InMemoryDataset
+
+
+class MedShapeNet(InMemoryDataset):
+    r"""The MedShapeNet datasets from the `"MedShapeNet -- A Large-Scale
+    Dataset of 3D Medical Shapes for Computer Vision"
+    <https://arxiv.org/abs/2308.16139>`_ paper,
+    containing 8 different type of structures (classes).
+
+    .. note::
+
+        Data objects hold mesh faces instead of edge indices.
+        To convert the mesh to a graph, use the
+        :obj:`torch_geometric.transforms.FaceToEdge` as :obj:`pre_transform`.
+        To convert the mesh to a point cloud, use the
+        :obj:`torch_geometric.transforms.SamplePoints` as :obj:`transform` to
+        sample a fixed number of points on the mesh faces according to their
+        face area.
+
+    Args:
+        root (str): Root directory where the dataset should be saved.
+        size (int): Number of invividual 3D structures to download per
+            type (classes).
+        transform (callable, optional): A function/transform that takes in an
+            :obj:`torch_geometric.data.Data` object and returns a transformed
+            version. The data object will be transformed before every access.
+            (default: :obj:`None`)
+        pre_transform (callable, optional): A function/transform that takes in
+            an :obj:`torch_geometric.data.Data` object and returns a
+            transformed version. The data object will be transformed before
+            being saved to disk. (default: :obj:`None`)
+        pre_filter (callable, optional): A function that takes in an
+            :obj:`torch_geometric.data.Data` object and returns a boolean
+            value, indicating whether the data object should be included in the
+            final dataset. (default: :obj:`None`)
+        force_reload (bool, optional): Whether to re-process the dataset.
+            (default: :obj:`False`)
+    """
+    def __init__(
+        self,
+        root: str,
+        size: int = 100,
+        transform: Optional[Callable] = None,
+        pre_transform: Optional[Callable] = None,
+        pre_filter: Optional[Callable] = None,
+        force_reload: bool = False,
+    ) -> None:
+        self.size = size
+        super().__init__(root, transform, pre_transform, pre_filter,
+                         force_reload=force_reload)
+
+        path = self.processed_paths[0]
+        self.load(path)
+
+    @property
+    def raw_file_names(self) -> List[str]:
+        return [
+            '3DTeethSeg', 'CoronaryArteries', 'FLARE', 'KITS', 'PULMONARY',
+            'SurgicalInstruments', 'ThoracicAorta_Saitta', 'ToothFairy'
+        ]
+
+    @property
+    def processed_file_names(self) -> List[str]:
+        return ['dataset.pt']
+
+    @property
+    def raw_paths(self) -> List[str]:
+        r"""The absolute filepaths that must be present in order to skip
+        downloading.
+        """
+        return [osp.join(self.raw_dir, f) for f in self.raw_file_names]
+
+    def process(self) -> None:
+        import urllib3
+        from MedShapeNet import MedShapeNet as msn
+
+        msn_instance = msn(timeout=120)
+
+        urllib3.HTTPConnectionPool("medshapenet.ddns.net", maxsize=50)
+
+        list_of_datasets = msn_instance.datasets(False)
+        list_of_datasets = list(
+            filter(
+                lambda x: x not in [
+                    'medshapenetcore/ASOCA', 'medshapenetcore/AVT',
+                    'medshapenetcore/AutoImplantCraniotomy',
+                    'medshapenetcore/FaceVR'
+                ], list_of_datasets))
+
+        subset = []
+        for dataset in list_of_datasets:
+            self.newpath = self.root + '/' + dataset.split("/")[1]
+            if not os.path.exists(self.newpath):
+                os.makedirs(self.newpath)
+            stl_files = msn_instance.dataset_files(dataset, '.stl')
+            subset.extend(stl_files[:self.size])
+
+            for stl_file in stl_files[:self.size]:
+                msn_instance.download_stl_as_numpy(bucket_name=dataset,
+                                                   stl_file=stl_file,
+                                                   output_dir=self.newpath,
+                                                   print_output=False)
+
+        class_mapping = {
+            '3DTeethSeg': 0,
+            'CoronaryArteries': 1,
+            'FLARE': 2,
+            'KITS': 3,
+            'PULMONARY': 4,
+            'SurgicalInstruments': 5,
+            'ThoracicAorta_Saitta': 6,
+            'ToothFairy': 7
+        }
+
+        for dataset, path in zip([subset], self.processed_paths):
+            data_list = []
+            for item in dataset:
+                class_name = item.split("/")[0]
+                item = item.split("stl")[0]
+                target = class_mapping[class_name]
+                file = osp.join(self.root, item + 'npz')
+
+                data = np.load(file)
+                pre_data_list = Data(
+                    pos=torch.tensor(data["vertices"], dtype=torch.float),
+                    face=torch.tensor(data["faces"],
+                                      dtype=torch.long).t().contiguous())
+                pre_data_list.y = torch.tensor([target], dtype=torch.long)
+                data_list.append(pre_data_list)
+
+            if self.pre_filter is not None:
+                data_list = [d for d in data_list if self.pre_filter(d)]
+
+            if self.pre_transform is not None:
+                data_list = [self.pre_transform(d) for d in data_list]
+
+            self.save(data_list, path)