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LCNAData.py

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+import os.path as osp
+import pandas as pd
+
+import torch
+from torch_geometric.data import Dataset, download_url
+
+
+class LCNAData(Dataset):
+    def __init__(self, root, transform=None, pre_transform=None, pre_filter=None):
+        super().__init__(root, transform, pre_transform, pre_filter)
+        self.data_labels = pd.read_csv(osp.join(root, 'data_labels.csv'))
+
+    def len(self):
+        return len(self.data_labels)
+
+    def get(self, idx):
+        subject_id = self.data_labels.iloc[idx]['subject_id']
+        protocol_label = self.data_labels.iloc[idx]['label']
+        sample_id = self.data_labels.iloc[idx]['sample_id']
+        stim_id = self.data_labels.iloc[idx]['stim_id']
+        data = torch.load(osp.join(self.root, str(subject_id), f'sub{subject_id}_prot{protocol_label}_stim{stim_id}_sample{sample_id}.pt'))
+        data.x = data.x.float()
+        data.edge_attr = data.edge_attr.float()
+        data.x[data.x == float('inf')] = 0
+        data.edge_attr[data.edge_attr == float('inf')] = 0
+        return data

env.yml

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+name: neuroimage
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - notebook=6.5
+  - nilearn
+  - nibabel
+  - mne
+  - mne-base
+  - mnelab
+  - mne-bids
+  - mne-nirs
+  - mne-icalabel
+  - mne-connectivity
+  - mne-faster
+  - mne-realtime
+  - mne-features
+  - nipype
+  - dipy
+  - fslpy
+  - fsleyes-widgets
+  - file-tree-fsl
+  - fsl-pyfeeds
+  - fsl-pipe
+  - fsleyes
+  - tqdm
+  - requests
+  - openneuro-py
+  - numpy
+  - matplotlib
+  - ipympl
+  - scipy
+  - pandas
+  - jupyterlab-myst
+  - jupyterlab-spellchecker
+  - jupyterlab-variableinspector
+  - pytorch=2[build=cuda*]
+  - torchvision
+  - torchaudio
+  - pytorch-cuda=11.8
+  - jupyterlab
+  - nb_conda_kernels
+  - jupyter_contrib_nbextensions
+  - aiofiles
+  - aiosqlite
+  - bottleneck
+  - brotlipy
+  - click
+  - cloudpickle
+  - cryptography
+  - cytoolz
+  - dask
+  - dill
+  - edflib-python
+  - file-tree
+  - fsleyes-props
+  - fsspec
+  - future
+  - graphql-core
+  - h11
+  - h2
+  - h5io
+  - h5py
+  - hpack
+  - httpcore
+  - httpx
+  - hyperframe
+  - imagecodecs
+  - imageio
+  - ipycanvas
+  - ipyevents
+  - ipyvtklink
+  - isodate
+  - jupyter_server_fileid
+  - jupyter_server_ydoc
+  - locket
+  - markdown-it-py
+  - mdurl
+  - mkl-service
+  - numexpr
+  - parse
+  - partd
+  - pathlib2
+  - patsy
+  - pooch
+  - progressbar2
+  - py-cpuinfo
+  - pyabel
+  - pybv
+  - pydicom
+  - pymatreader
+  - pyopengl
+  - pyopenssl
+  - pypubsub
+  - python-utils
+  - pywavelets
+  - rich
+  - rtree
+  - scikit-image
+  - seaborn
+  - sgqlc
+  - statsmodels
+  - tifffile
+  - toolz
+  - trimesh
+  - wxnatpy
+  - wxpython
+  - xarray
+  - xmltodict
+  - xnat
+  - y-py
+  - ypy-websocket
+  - pyg
+  - ca-certificates
+  - openssl
+  - tensorly
+  - certifi
+  - ants==2.4.4
+  - libitk-devel
+  - simpleitk
+  - itk
+  - gdown
+  - pytorch_sparse
+  - python-lsp-server
+  - tensorboard
+  - tensorboardx
+prefix: /home/arashsm79/.miniforge3/envs/neuroimage