Pr/wsi enhance operator

runtime/ops/mapper/__init__.py

@@ -63,5 +63,6 @@ def _import_operators():
     from . import video_speech_asr
     from . import video_subtitle_ocr
     from . import video_text_ocr
+    from . import wsi_enhance_operator
 
 _import_operators()

runtime/ops/mapper/wsi_enhance_operator/README.md

@@ -0,0 +1,136 @@
+# WSIEnhance Operator
+
+## Overview
+
+`wsi_enhance_operator` is a custom mapper operator package for DataMate.
+
+It includes:
+
+- operator registration entry
+- operator metadata and UI settings
+- main pipeline implementation
+- WSI reading helpers
+- slide segmentation helpers
+- patch extraction helpers
+- stain normalization helpers
+- augmentation helpers
+
+## Directory Structure
+
+```text
+wsi_enhance_operator/
+├── __init__.py
+├── metadata.yml
+├── process.py
+├── README.md
+├── requirements.txt
+├── augmentations/
+│   ├── __init__.py
+│   └── augmentations.py
+├── slidesegmenter/
+│   ├── __init__.py
+│   ├── _model_utils.py
+│   ├── slidesegmenter.py
+│   └── model_files/
+│       └── __init__.py
+├── stain_normalization/
+│   ├── __init__.py
+│   └── stain_normalization.py
+├── wsi_processor/
+│   ├── __init__.py
+│   └── wsi_processor.py
+└── wsi_reader/
+    ├── __init__.py
+    ├── wsi_reader.py
+    └── wsi_types.py
+```
+
+## File Responsibilities
+
+- `__init__.py`: registers `WSIEnhanceMapper` into DataMate operator registry
+- `metadata.yml`: defines operator identity, category, runtime resources, and frontend settings
+- `process.py`: main mapper entry, parameter parsing, segmentation, patch extraction, and artifact export
+- `augmentations/`: patch augmentation utilities
+- `slidesegmenter/`: segmentation model loading and inference helpers
+- `stain_normalization/`: stain normalization logic
+- `wsi_processor/`: contour and detection post-processing helpers
+- `wsi_reader/`: WSI file reading abstraction
+- `requirements.txt`: Python dependencies required by this operator package
+
+## Model Path
+
+The runtime environment is expected to provide model files under:
+
+- `/models/WSIEnhance/<model_folder>`
+
+Default `model_folder`:
+
+- `2025-10-18`
+
+## Input Expectations
+
+The operator accepts a `sample` dictionary. Common supported input fields are:
+
+- `filePath`: source WSI path
+- `image_path`: source WSI path alias
+- `source_path`: optional source path alias
+- `export_path`, `exportPath`, or `output_dir`: output root directory
+
+## Main Settings
+
+Common configurable settings in `metadata.yml` include:
+
+- `model_folder`
+- `thumbnail_size`
+- `patch_size`
+- `patch_bg_thresh`
+- `patch_max_bg_ratio`
+- `save_patches`
+- `enable_stain_normalize`
+- `save_normalized_patches`
+- `stain_method`
+- `stain_target`
+- `enable_augmentation`
+- `save_augmented_patches`
+- `aug_factor`
+- `aug_rotate`
+- `aug_flip`
+- `aug_color_jitter`
+
+## Output Layout
+
+For each input slide, the operator can generate:
+
+- `segmentation/thumbnail.png`
+- `segmentation/thumbnail_overlay.png`
+- `segmentation/coords_thumbnail.json`
+- `patch_extract/patch_positions.json`
+- `patch_extract/pipeline_manifest.json`
+- `patch_extract/patches/` when raw patch saving is enabled
+- `patch_extract/patches_normalized/` when stain normalization output saving is enabled
+- `patch_extract/patches_augmented/` when augmentation output saving is enabled
+
+## Output Fields
+
+The operator writes result paths and summary fields back into `sample`. Common output fields include:
+
+- `thumbnail_path`
+- `thumbnail_overlay_path`
+- `coords_thumbnail_json`
+- `patch_positions_json`
+- `pipeline_manifest_json`
+- `patch_count`
+- `normalized_patch_count`
+- `augmented_count`
+- `patches_dir`
+- `normalized_patches_dir`
+- `augmented_patches_dir`
+
+## Usage Notes
+
+1. Place the operator directory under `runtime/ops/mapper/wsi_enhance_operator`.
+2. Ensure `metadata.yml`, `process.py`, and `__init__.py` are present.
+3. Ensure required WSI runtime dependencies are installed, including OpenSlide-related dependencies.
+4. Ensure model files are mounted under `/models/WSIEnhance/<model_folder>`.
+5. Import the operator package from `runtime/ops/mapper/__init__.py`.
+6. Configure parameters from the DataMate frontend or task definition.

runtime/ops/mapper/wsi_enhance_operator/__init__.py

@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+"""
+WSIEnhance 全幻灯片成像处理算子注册入口
+"""
+
+from datamate.core.base_op import OPERATORS
+
+OPERATORS.register_module(
+    module_name='WSIEnhanceMapper',
+    module_path="ops.mapper.wsi_enhance_operator.process"
+)

runtime/ops/mapper/wsi_enhance_operator/augmentations/__init__.py

@@ -0,0 +1,7 @@
+"""
+数据增强模块
+"""
+
+from .augmentations import Augmenter, AugmentationConfig
+
+__all__ = ["Augmenter", "AugmentationConfig"]