Extracts collagen features from MuTIsWSIRunner ouput.
| 44 | |
| 45 | |
| 46 | class SlideCollagenFeatureExtractor(object): |
| 47 | """ |
| 48 | Extracts collagen features from MuTIsWSIRunner ouput. |
| 49 | """ |
| 50 | def __init__( |
| 51 | self, |
| 52 | slide_dir: str, |
| 53 | output_dir: str, |
| 54 | wsi_file: str, |
| 55 | *, |
| 56 | slide_name: str = None, |
| 57 | mpp: float = 0.5, |
| 58 | roi_size: int = 512, |
| 59 | topk_salient_rois: int = 256, |
| 60 | min_stroma_ratio=0.3, |
| 61 | min_tumor_ratio=0.2, |
| 62 | region_prop_names: Iterable[str] = None, |
| 63 | max_axis_ratio_for_fiber=0.2, |
| 64 | monitor: str = "", |
| 65 | logger: Any = None, |
| 66 | _region_class_map: Dict[str, str] = None, |
| 67 | _nucleus_class_map: Dict[str, str] = None, |
| 68 | _debug: bool = False, |
| 69 | ): |
| 70 | """ |
| 71 | This represents the slide as a feature matrix summarizing |
| 72 | the collagen with tumor-associated stroma. |
| 73 | """ |
| 74 | self.slide_dir = slide_dir |
| 75 | self.output_dir = output_dir |
| 76 | self.wsi_file = wsi_file |
| 77 | self.slide_name = slide_name or os.path.basename(slide_dir) |
| 78 | self.mpp = mpp |
| 79 | self.roi_size = roi_size |
| 80 | self.topk_salient_rois = topk_salient_rois |
| 81 | self.min_stroma_ratio = min_stroma_ratio |
| 82 | self.min_tumor_ratio = min_tumor_ratio |
| 83 | self.max_axis_ratio_for_fiber = max_axis_ratio_for_fiber |
| 84 | self.monitor = monitor |
| 85 | self.logger = logger or logging.getLogger(__name__) |
| 86 | self._debug = _debug |
| 87 | |
| 88 | # codes and class map for most relevant classes |
| 89 | self._region_class_map = _region_class_map or { |
| 90 | 'TILS': 'STROMA', # tils-dense stroma is still stroma! |
| 91 | } |
| 92 | self._rcd = RegionCellCombination.REGION_CODES |
| 93 | self._nucleus_class_map = _nucleus_class_map or { |
| 94 | 'ActiveStromalCellNOS': 'StromalCellNOS', |
| 95 | } |
| 96 | self._ncd = RegionCellCombination.NUCLEUS_CODES |
| 97 | |
| 98 | # region props to extract per collagen fibril edge |
| 99 | self._region_prop_names = region_prop_names or ( |
| 100 | 'label', |
| 101 | 'area', # fibril edge length -- a bit noisy d.t. looping |
| 102 | 'major_axis_length', # more robust than area visually |
| 103 | 'minor_axis_length', |
no outgoing calls
no test coverage detected