Add tool for evaluation of tissue geometry properties #21

lazyslide/tl/tissue_props.py

@@ -0,0 +1,163 @@
+import cv2
+import numpy as np
+from functools import cached_property
+
+import pandas as pd
+
+from lazyslide.wsi import WSI
+from lazyslide.get import tissue_contours
+
+
+def tissue_props(
+    wsi: WSI,
+    key: str = "tissue",
+):
+    """Extract tissue properties from the WSI."""
+    props = []
+    cnts = []
+    for tissue_contour in tissue_contours(wsi, key=key, return_type="numpy"):
+        cnt = tissue_contour.contour
+        holes = tissue_contour.holes
+        _props = TissueProps(cnt, holes)()
+        cnts.append(cnt)
+        _props["tissue_id"] = tissue_contour.id
+        props.append(_props)
+
+    wsi.add_contours(cnts, data=pd.DataFrame(props), name=f"{key}_contours")
+
+
+class TissueProps:
+    def __init__(self, cnt, holes=None):
+        self.cnt = cnt
+        self.holes = holes
+
+    @cached_property
+    def area_filled(self):
+        return cv2.contourArea(self.cnt)
+
+    @cached_property
+    def area(self):
+        """Area without holes."""
+        if self.holes is None:
+            return self.area_filled
+        else:
+            area = self.area_filled
+            for hole in self.holes:
+                area -= cv2.contourArea(hole)
+            return area
+
+    @cached_property
+    def bbox(self):
+        x, y, w, h = cv2.boundingRect(self.cnt)
+        return x, y, w, h
+
+    @cached_property
+    def centroid(self):
+        M = self.moments
+        cX = int(M["m10"] / M["m00"])
+        cY = int(M["m01"] / M["m00"])
+        return cX, cY
+
+    @cached_property
+    def convex_hull(self):
+        return cv2.convexHull(self.cnt)
+
+    @cached_property
+    def convex_area(self):
+        return cv2.contourArea(self.convex_hull)
+
+    @cached_property
+    def solidity(self):
+        """Solidity is the ratio of the contour area to the convex area."""
+        if self.convex_area == 0:
+            return 0
+        return self.area / self.convex_area
+
+    @cached_property
+    def convexity(self):
+        """Convexity is the ratio of the convex area to the contour area."""
+        if self.area == 0:
+            return 0
+        return self.convex_area / self.area
+
+    @cached_property
+    def ellipse(self):
+        return cv2.fitEllipse(self.cnt)
+
+    @cached_property
+    def axis_major_length(self):
+        x1, x2 = self.ellipse[1]
+        if x1 < x2:
+            return x2
+        return x1
+
+    @cached_property
+    def axis_minor_length(self):
+        x1, x2 = self.ellipse[1]
+        if x1 < x2:
+            return x1
+        return x2
+
+    @cached_property
+    def eccentricity(self):
+        if self.axis_major_length == 0:
+            return 0
+        return np.sqrt(1 - (self.axis_minor_length**2) / (self.axis_major_length**2))
+
+    @cached_property
+    def orientation(self):
+        return self.ellipse[2]
+
+    @cached_property
+    def extent(self):
+        if self.area == 0:
+            return 0
+        return self.area / (self.bbox[2] * self.bbox[3])
+
+    @cached_property
+    def perimeter(self):
+        return cv2.arcLength(self.cnt, True)
+
+    @cached_property
+    def circularity(self):
+        if self.perimeter == 0:
+            return 0
+        return 4 * np.pi * self.area / (self.perimeter**2)
+
+    @cached_property
+    def moments(self):
+        return cv2.moments(self.cnt)
+
+    @cached_property
+    def moments_hu(self):
+        return cv2.HuMoments(self.moments)
+
+    def __call__(self):
+        props = {
+            "area": self.area,
+            "area_filled": self.area_filled,
+            "convex_area": self.convex_area,
+            "solidity": self.solidity,
+            "convexity": self.convexity,
+            "axis_major_length": self.axis_major_length,
+            "axis_minor_length": self.axis_minor_length,
+            "eccentricity": self.eccentricity,
+            "orientation": self.orientation,
+            "extent": self.extent,
+            "perimeter": self.perimeter,
+            "circularity": self.circularity,
+        }
+
+        for ix, box in enumerate(self.bbox):
+            props[f"bbox-{ix}"] = box
+
+        for ix, c in enumerate(self.centroid):
+            props[f"centroid-{ix}"] = c
+
+        for i, hu in enumerate(self.moments_hu):
+            props[f"hu-{i}"] = hu[0]
+
+        for key, value in self.moments.items():
+            props[f"moment-{key}"] = value
+
+        return props