Metadata-Version: 2.1
Name: slicerio
Version: 0.1.3
Summary: Utilities for 3D Slicer
Home-page: https://github.com/lassoan/slicerio
Author: Andras Lasso
Author-email: lasso@queensu.ca
Maintainer: Andras Lasso
Maintainer-email: lasso@queensu.ca
License: UNKNOWN
Download-URL: https://github.com/lassoan/slicerio/archive/master.zip
Description: [![Python package](https://github.com/lassoan/slicerio/workflows/Python%20package/badge.svg)](https://github.com/lassoan/slicerio/actions?query=workflow%3A%22Python+package%22)
        ![Upload Python Package](https://github.com/lassoan/slicerio/workflows/Upload%20Python%20Package/badge.svg)
        [![PyPI version](https://badge.fury.io/py/slicerio.svg)](https://badge.fury.io/py/slicerio)
        
        # *slicerio*
        
        Python utilities for [3D Slicer](https://www.slicer.org) interoperability.
        
        The package contains utility functions for reading and writing segmentation files.
        More functions will be added in the future.
        
        ## Installation
        
        Using [pip](https://pip.pypa.io/en/stable/):
        
        ```
        pip install slicerio
        ```
        
        ## Examples
        
        ### Read segmentation and show some information about segments
        
        ```python
        import slicerio
        import json
        
        segmentation_info = slicerio.read_segmentation_info("Segmentation.seg.nrrd")
        
        number_of_segments = len(segmentation_info["segments"])
        print(f"Number of segments: {number_of_segments}")
        
        segment_names = slicerio.segment_names(segmentation_info)
        print(f"Segment names: {', '.join(segment_names)}")
        
        segment0 = slicerio.segment_from_name(segmentation_info, segment_names[0])
        print("First segment info:\n" + json.dumps(segment0, sort_keys=False, indent=4))
        ```
        
        ### Extract selected segments with chosen label values
        
        ```python
        import slicerio
        import nrrd
        
        input_filename = "path/to/Segmentation.seg.nrrd"
        output_filename = "path/to/SegmentationExtracted.seg.nrrd"
        segment_names_to_labels = [("ribs", 10), ("right lung", 12), ("left lung", 6)]
        
        voxels, header = nrrd.read(input_filename)
        extracted_voxels, extracted_header = slicerio.extract_segments(voxels, header, segmentation_info, segment_names_to_labels)
        nrrd.write(output_filename, extracted_voxels, extracted_header)
        ```
        
Keywords: 3DSlicer medical imaging segmentation
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: System :: Networking
Requires-Python: >=3.6
Description-Content-Type: text/markdown
