Metadata-Version: 2.1
Name: slicerio
Version: 0.1.4
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 and convenience functions for using 3D Slicer via its web API. 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)
        ```
        
        ### View files in 3D Slicer
        
        It is useful to load several files in a single Slicer instance, because then there is no need to wait for multiple
        application startups and multiple data sets can be compared in one environment. This can be achieved by activating
        3D Slicer's Web Server module, which provides a web API to control the application.
        
        For example, an image file can be loaded with the command below. The command starts a new Slicer application instance
        with the web API enabled.
        
        ```python
        import slicerio
        import os
        slicerio.view_file("path/to/SomeImage.nrrd", slicer_executable=f"{os.environ["LOCALAPPDATA"]}/NA-MIC/Slicer 5.2.0/Slicer.exe")
        ```
        
        A segmentation file can be loaded in the same Slicer instance:
        
        ```python
        import slicerio
        slicerio.view_file("path/to/Segmentation.seg.nrrd", "SegmentationFile")
        ```
        
        Supported file types:
        - image files (nrrd, nii.gz, ...): `VolumeFile`
        - segmentation file (.seg.nrrd, nrrd, nii.gz, ...): `SegmentationFile`
        - model file (.stl, .ply, .vtk, .vtp, .vtu, ...): `ModelFile`
        - markup file (.mrj.json): `MarkupsFile`
        - transform file (.tfm, .h5, .txt): `TransformFile`
        - spreadsheet file (.csv, .tsv): `TableFile`
        - text file (.txt, .json, ...): `TextFile`
        - sequence file (.mrb, .seq.nrrd): `SequenceFile`
        - Slicer scene file (.mrml, .mrb): `SceneFile`
        
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
