histotuner 0.1.0__tar.gz

histotuner-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: histotuner
+Version: 0.1.0
+Summary: Add your description here
+Author: Ajit Johnson Nirmal
+Author-email: Ajit Johnson Nirmal <ajitjohnson.n@gmail.com>
+Requires-Dist: anndata>=0.12.2
+Requires-Dist: cellpose>=4.0.6
+Requires-Dist: dask>=2024.11.2
+Requires-Dist: geopandas>=1.1.1
+Requires-Dist: matplotlib>=3.10.6
+Requires-Dist: numpy>=2.3.3
+Requires-Dist: opencv-python>=4.11.0.86
+Requires-Dist: openslide-bin>=4.0.0.8
+Requires-Dist: openslide-python>=1.4.2
+Requires-Dist: pillow>=11.3.0
+Requires-Dist: pip>=25.2
+Requires-Dist: psutil>=7.1.0
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: scikit-learn>=1.7.2
+Requires-Dist: shapely>=2.1.2
+Requires-Dist: spatialdata>=0.5.0
+Requires-Dist: tifffile>=2025.9.30
+Requires-Dist: timm>=1.0.20
+Requires-Dist: transformers>=4.57.1
+Requires-Dist: wandb>=0.22.2
+Requires-Dist: zarr>=2.18.7
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+

histotuner-0.1.0/pyproject.toml

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+[project]
+name = "histotuner"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+authors = [
+    { name = "Ajit Johnson Nirmal", email = "ajitjohnson.n@gmail.com" }
+]
+requires-python = ">=3.12"
+dependencies = [
+    "anndata>=0.12.2",
+    "cellpose>=4.0.6",
+    "dask>=2024.11.2",
+    "geopandas>=1.1.1",
+    "matplotlib>=3.10.6",
+    "numpy>=2.3.3",
+    "opencv-python>=4.11.0.86",
+    "openslide-bin>=4.0.0.8",
+    "openslide-python>=1.4.2",
+    "pillow>=11.3.0",
+    "pip>=25.2",
+    "psutil>=7.1.0",
+    "pyyaml>=6.0.3",
+    "scikit-learn>=1.7.2",
+    "shapely>=2.1.2",
+    "spatialdata>=0.5.0",
+    "tifffile>=2025.9.30",
+    "timm>=1.0.20",
+    "transformers>=4.57.1",
+    "wandb>=0.22.2",
+    "zarr>=2.18.7",
+]
+
+[build-system]
+requires = ["uv_build>=0.8.14,<0.9.0"]
+build-backend = "uv_build"

histotuner-0.1.0/src/histotuner/__init__.py

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+import sys
+
+# Version
+try:
+    from importlib.metadata import version as _pkg_version
+    __version__ = _pkg_version("histotuner")
+except Exception:
+    __version__ = "unknown"
+
+# Print only histotuner version on import
+print(f"histotuner {__version__}")
+
+# Provide a friendly greeting
+
+def hello() -> str:
+    return "Hello from histotuner!"
+
+# Lightweight import (safe)
+try:
+    from .crop_image import cropImage  # lightweight
+except Exception:
+    # Lazy fallback to avoid noisy import-time errors
+    def cropImage(*args, **kwargs):
+        from .crop_image import cropImage as _fn
+        return _fn(*args, **kwargs)
+
+# Heavy deps: define lazy wrappers to avoid import-time initialization/prints (e.g., cellpose)
+
+def segmentImage(*args, **kwargs):
+    from .segment import segmentImage as _fn
+    return _fn(*args, **kwargs)
+
+# Tissue helpers (cv2/geopandas/shapely may be heavy): lazy wrappers
+
+def tissueMask(*args, **kwargs):
+    from .tissue import tissueMask as _fn
+    return _fn(*args, **kwargs)
+
+def generateTissueMask(*args, **kwargs):
+    from .tissue import generateTissueMask as _fn
+    return _fn(*args, **kwargs)
+
+def BinaryMask(*args, **kwargs):
+    from .tissue import BinaryMask as _fn
+    return _fn(*args, **kwargs)
+
+def binaryMaskToPolygons(*args, **kwargs):
+    from .tissue import binaryMaskToPolygons as _fn
+    return _fn(*args, **kwargs)
+
+def binaryMaskToPolygonsWithProb(*args, **kwargs):
+    from .tissue import binaryMaskToPolygonsWithProb as _fn
+    return _fn(*args, **kwargs)
+
+def overlayTissueThumbnail(*args, **kwargs):
+    from .tissue import overlayTissueThumbnail as _fn
+    return _fn(*args, **kwargs)
+
+# Embedding pipeline: lazy wrappers
+
+def load_config(*args, **kwargs):
+    from .embedImage import load_config as _fn
+    return _fn(*args, **kwargs)
+
+def loadHistoEmbedConfig(*args, **kwargs):
+    """Alias for embedding config loader to avoid confusion with training config."""
+    from .embedImage import load_config as _fn
+    return _fn(*args, **kwargs)
+
+def runEmbeddingPipeline(*args, **kwargs):
+    from .embedImage import runEmbeddingPipeline as _fn
+    return _fn(*args, **kwargs)
+
+def embedImageFromDict(*args, **kwargs):
+    from .embedImage import embedImageFromDict as _fn
+    return _fn(*args, **kwargs)
+
+def embedImageFromYaml(*args, **kwargs):
+    from .embedImage import embedImageFromYaml as _fn
+    return _fn(*args, **kwargs)
+
+# Training helpers (histotune): lazy wrappers
+
+def loadHistotuneConfig(*args, **kwargs):
+    from .histotune import load_config as _fn
+    return _fn(*args, **kwargs)
+
+def runHistotunePipeline(*args, **kwargs):
+    from .histotune import runTrainingPipeline as _fn
+    return _fn(*args, **kwargs)
+
+def runHistotuneFromYaml(*args, **kwargs):
+    from .histotune import runTrainingFromYaml as _fn
+    return _fn(*args, **kwargs)
+
+def runHistotuneTraining(*args, **kwargs):
+    from .histotune import run_training as _fn
+    return _fn(*args, **kwargs)
+
+# Spatial feature table helpers: lazy wrappers
+
+def spatialFeatureTable(*args, **kwargs):
+    from .spatialfeaturetable import spatialFeatureTable as _fn
+    return _fn(*args, **kwargs)
+
+def spatialFeatureTableFromDict(*args, **kwargs):
+    from .spatialfeaturetable import spatialFeatureTableFromDict as _fn
+    return _fn(*args, **kwargs)
+
+# Token→cell mapper utilities: lazy wrappers
+
+def token_to_cell_mapper(*args, **kwargs):
+    from .token_cell_mapper import token_to_cell_mapper as _fn
+    return _fn(*args, **kwargs)
+
+def attach_token_cell_alignment(*args, **kwargs):
+    from .token_cell_mapper import attach_token_cell_alignment as _fn
+    return _fn(*args, **kwargs)
+
+def save_spatialdata_to_zarr(*args, **kwargs):
+    from .token_cell_mapper import save_spatialdata_to_zarr as _fn
+    return _fn(*args, **kwargs)
+
+def tokenCellMapper(*args, **kwargs):
+    from .token_cell_mapper import tokenCellMapper as _fn
+    return _fn(*args, **kwargs)
+
+# Cell phenotype mapper utilities: lazy wrappers
+
+def attach_cell_phenotype(*args, **kwargs):
+    from .cell_phenotype_mapper import attach_cell_phenotype as _fn
+    return _fn(*args, **kwargs)
+
+def attach_cell_phenotype_to_zarr(*args, **kwargs):
+    from .cell_phenotype_mapper import attach_cell_phenotype_to_zarr as _fn
+    return _fn(*args, **kwargs)
+
+def cellPhenotypeMapper(*args, **kwargs):
+    from .cell_phenotype_mapper import cellPhenotypeMapper as _fn
+    return _fn(*args, **kwargs)
+
+def phenotypeCellMapper(*args, **kwargs):
+    from .cell_phenotype_mapper import phenotypeCellMapper as _fn
+    return _fn(*args, **kwargs)
+
+__all__ = [
+    "__version__",
+    "hello",
+    "cropImage",
+    "segmentImage",
+    "tissueMask",
+    "generateTissueMask",
+    "BinaryMask",
+    "binaryMaskToPolygons",
+    "binaryMaskToPolygonsWithProb",
+    "overlayTissueThumbnail",
+    # Embedding pipeline (image)
+    "load_config",
+    "loadHistoEmbedConfig",
+    "runEmbeddingPipeline",
+    "embedImageFromDict",
+    "embedImageFromYaml",
+    # Training pipeline (histotune)
+    "loadHistotuneConfig",
+    "runHistotunePipeline",
+    "runHistotuneFromYaml",
+    "runHistotuneTraining",
+    # Spatial feature table and mappers
+    "spatialFeatureTable",
+    "spatialFeatureTableFromDict",
+    "token_to_cell_mapper",
+    "attach_token_cell_alignment",
+    "save_spatialdata_to_zarr",
+    "tokenCellMapper",
+    "attach_cell_phenotype",
+    "attach_cell_phenotype_to_zarr",
+    "cellPhenotypeMapper",
+    "phenotypeCellMapper",
+]