scalesurfer 0.1.0__tar.gz

scalesurfer-0.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+.venv
+*.svg
+*.mgz
+*.png
+*.csv
+*cache*
+*checkpoints*
+* copy*

scalesurfer-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: scalesurfer
+Version: 0.1.0
+Summary: Fast 3D brain segmentation and FreeSurfer-like statistics inference.
+Project-URL: Homepage, https://github.com/voytekresearch/scalesurfer
+Project-URL: Repository, https://github.com/voytekresearch/scalesurfer
+Project-URL: Issues, https://github.com/voytekresearch/scalesurfer/issues
+Author: Ryan Hammonds
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.12
+Requires-Dist: huggingface-hub
+Requires-Dist: joblib
+Requires-Dist: matplotlib
+Requires-Dist: nibabel
+Requires-Dist: nilearn
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: safetensors
+Requires-Dist: scikit-image
+Requires-Dist: scipy
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: torch
+Requires-Dist: tqdm
+Provides-Extra: openneuro
+Requires-Dist: boto3; extra == 'openneuro'
+Requires-Dist: botocore; extra == 'openneuro'
+Requires-Dist: joblib; extra == 'openneuro'
+Requires-Dist: matplotlib; extra == 'openneuro'
+Requires-Dist: nibabel; extra == 'openneuro'
+Requires-Dist: nilearn; extra == 'openneuro'
+Requires-Dist: numba; extra == 'openneuro'
+Requires-Dist: numpy; extra == 'openneuro'
+Requires-Dist: pandas; extra == 'openneuro'
+Requires-Dist: scikit-image; extra == 'openneuro'
+Requires-Dist: scipy; extra == 'openneuro'
+Requires-Dist: torch; extra == 'openneuro'
+Requires-Dist: tqdm; extra == 'openneuro'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# scalesufer
+
+`scalesurfer` is a repository for fast FreeSurfer inference. The volumetric model uses UNet (local scale), with a Transformer bottlenck (global scale). The stats models predict FreeSurfer stats.
+
+## Usage
+
+```python
+from scalesurfer import ScaleSurfer
+
+# Anatomical images
+adni_dir = "/home/rph/scalesurfer/data/adni_bids"
+subjects = ["sub-002S0559", "sub-002S0619"]
+
+anat_files = [
+    f"{adni_dir}/sub-002S0559/ses-20060627/anat/sub-002S0559_ses-20060627_T1w.nii.gz",
+    f"{adni_dir}/sub-002S0619/ses-20060601/anat/sub-002S0619_ses-20060601_T1w.nii.gz"
+]
+
+# Predict aparc+aseg and stats tables
+surfer = ScaleSurfer(anat_files, subjects, "/tmp/scalesurfer_subjects", device="cuda")
+surfer.prepare_images()
+surfer.predict_volumes()
+surfer.plot_volume(subjects[0])
+df_stats = surfer.predict_stats()
+```
+
+See the inference [notebook](https://github.com/voytekresearch/scalesurfer/blob/master/docs/notebooks/03_inference/08_inference.ipynb) for additional settings for faster processing.

scalesurfer-0.1.0/README.md

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+# scalesufer
+
+`scalesurfer` is a repository for fast FreeSurfer inference. The volumetric model uses UNet (local scale), with a Transformer bottlenck (global scale). The stats models predict FreeSurfer stats.
+
+## Usage
+
+```python
+from scalesurfer import ScaleSurfer
+
+# Anatomical images
+adni_dir = "/home/rph/scalesurfer/data/adni_bids"
+subjects = ["sub-002S0559", "sub-002S0619"]
+
+anat_files = [
+    f"{adni_dir}/sub-002S0559/ses-20060627/anat/sub-002S0559_ses-20060627_T1w.nii.gz",
+    f"{adni_dir}/sub-002S0619/ses-20060601/anat/sub-002S0619_ses-20060601_T1w.nii.gz"
+]
+
+# Predict aparc+aseg and stats tables
+surfer = ScaleSurfer(anat_files, subjects, "/tmp/scalesurfer_subjects", device="cuda")
+surfer.prepare_images()
+surfer.predict_volumes()
+surfer.plot_volume(subjects[0])
+df_stats = surfer.predict_stats()
+```
+
+See the inference [notebook](https://github.com/voytekresearch/scalesurfer/blob/master/docs/notebooks/03_inference/08_inference.ipynb) for additional settings for faster processing.

scalesurfer-0.1.0/pyproject.toml

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+[project]
+name = "scalesurfer"
+version = "0.1.0"
+description = "Fast 3D brain segmentation and FreeSurfer-like statistics inference."
+readme = "README.md"
+requires-python = ">=3.12"
+authors = [
+    {name = "Ryan Hammonds"},
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "huggingface-hub",
+    "joblib",
+    "matplotlib",
+    "nibabel",
+    "nilearn",
+    "numba",
+    "numpy",
+    "pandas",
+    "safetensors",
+    "scikit-image",
+    "scipy",
+    "seaborn>=0.13.2",
+    "torch",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+
+openneuro = [
+    "boto3",
+    "botocore",
+    "joblib",
+    "matplotlib",
+    "nibabel",
+    "nilearn",
+    "numba",
+    "numpy",
+    "pandas",
+    "scikit-image",
+    "scipy",
+    "torch",
+    "tqdm",
+]
+
+[project.urls]
+Homepage = "https://github.com/voytekresearch/scalesurfer"
+Repository = "https://github.com/voytekresearch/scalesurfer"
+Issues = "https://github.com/voytekresearch/scalesurfer/issues"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["scalesurfer"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/scalesurfer",
+    "/README.md",
+    "/pyproject.toml",
+]

scalesurfer-0.1.0/scalesurfer/__init__.py

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+from scalesurfer.models.hub import fetch_all_models
+from scalesurfer.scalesurfer import ScaleSurfer
+
+__all__ = ["ScaleSurfer", "fetch_all_models"]