histopath/tool/tool_description/pathology.py

description = [
    {
        "description": "Perform zero-shot classification on a whole slide image",
        "name": "zero_shot_classification",
        "optional_parameters": [
            {
                "default": "./output",
                "description": "Directory to save output files",
                "name": "output_dir",
                "type": "str"
            }
        ],
        "required_parameters": [
            {
                "default": None,
                "description": "File path of the whole slide image",
                "name": "image_path",
                "type": "str"
            },
            {
                "default": None,
                "description": "Labels of the classes to perform zero-shot classification",
                "name": "labels",
                "type": "list"
            }
        ]
    },
    {
        "description": "Segment a Whole Slide Image (WSI)",
        "name": "segment_slide",
        "optional_parameters": [
            {
                "default": "./output",
                "description": "Directory to save output files",
                "name": "output_dir",
                "type": "str"
            }
        ],
        "required_parameters": [
            {
                "default": None,
                "description": "Path of the whole slide image",
                "name": "image_path",
                "type": "str"
            },
            {
                "default": None,
                "description": "Type of segmentation to perform",
                "name": "seg_type",
                "type": "str"
            },
            {
                "default": None,
                "description": "Segmentation model to use",
                "name": "model",
                "type": "str"
            }
        ]
    },
    {
        "description": "Quantify Fibrosis from a Whole Slide Image",
        "name": "quantify_fibrosis",
        "optional_parameters": [
            {
                "default": "./output",
                "description": "Directory to save output files",
                "name": "output_dir",
                "type": "str"
            },
            {
                "default": "grandqc",
                "description": "Tissue segmentation model to use (default: grandqc)",
                "name": "model",
                "type": "str"
            }
        ],
        "required_parameters": [
            {
                "default": None,
                "description": "Path to the whole slide image",
                "name": "image_path",
                "type": "str"
            }   
        ]
    },
    {
        "description": "Caption a whole slide image directly from the slide file or via tiled tissue patches from the slide file",
        "name": "caption_slide",
        "optional_parameters": [
            {
                "default": "./output",
                "description": "Directory to save output files",
                "name": "output_dir",
                "type": "str"
            },
            {
                "default": "Diagnosis:",
                "description": "Starting prompt of the generated caption ",
                "name": "prompt",
                "type": "str"
            }
        ],
        "required_parameters": [
            {
                "default": None,
                "description": "Path to the whole slide image",
                "name": "image_path",
                "type": "str"
            },
            {
                "default": None,
                "description": "Name of the whole slide image file",
                "name": "slide_name",
                "type": "str"
            } 
        ]
    }
]
    # {
    #     "description": "Quantify Tumor-Infiltrating Lymphocytes from "
    #     "whole slide image data via identification of inflammed nuclei "
    #     "region fractions and density"
    #     "name": "quantify_tumor_infilitrating_lymphocytes",
    #     "optional_parameters": [
    #         {
    #             "default": "./output",
    #             "description": "Directory to save output files"
    #             "name": "output_dir",
    #             "type": "str
    #         },
    #         {
    #             "default": ""
    #             "description": "",
    #             "name": ""
    #             "type": ""
    #         },
    #         {
    #             "default": ""
    #             "description": "",
    #             "name": ""
    #             "type": ""
    #         },
    #         {
    #             "default": ""
    #             "description": "",
    #             "name": ""
    #             "type": ""
    #         },
    #     ],
    #     "required_parameters": [
    #         "default": None,
    #         "description": "Path to the whole slide image",
    #         "name": "image_path",
    #         "type": "str"
    #     ],
    # },