histoseg 0.1.7__py3-none-any.whl → 0.1.8.1__py3-none-any.whl

histoseg/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.7'
-__version_tuple__ = version_tuple = (0, 1, 7)
+__version__ = version = '0.1.8.1'
+__version_tuple__ = version_tuple = (0, 1, 8, 1)
 
 __commit_id__ = commit_id = None

histoseg/geometry/__init__.py

@@ -0,0 +1,5 @@
+from .tissue_boundary import generate_tissue_boundary
+
+__all__ = [
+    "generate_tissue_boundary",
+]

histoseg/geometry/tissue_boundary.py

@@ -0,0 +1,141 @@
+import numpy as np
+import pandas as pd
+from shapely.geometry import MultiPoint, Polygon, MultiPolygon
+from shapely.ops import unary_union, triangulate
+
+
+def _alpha_shape(points, alpha):
+    """
+    Compute an alpha shape (concave hull) from a set of 2D points.
+
+    Parameters
+    ----------
+    points : np.ndarray of shape (n_points, 2)
+    alpha : float
+
+    Returns
+    -------
+    shapely.geometry.Polygon or MultiPolygon
+    """
+    if len(points) < 4:
+        return MultiPoint(points).convex_hull
+
+    triangles = triangulate(MultiPoint(points))
+    kept = []
+
+    for tri in triangles:
+        coords = np.array(tri.exterior.coords[:3])
+        a, b, c = coords
+
+        side_lengths = [
+            np.linalg.norm(a - b),
+            np.linalg.norm(b - c),
+            np.linalg.norm(c - a),
+        ]
+
+        s = sum(side_lengths) / 2.0
+        area_sq = (
+            s
+            * (s - side_lengths[0])
+            * (s - side_lengths[1])
+            * (s - side_lengths[2])
+        )
+
+        if area_sq <= 0:
+            continue
+
+        area = np.sqrt(area_sq)
+        circumradius = (
+            side_lengths[0] * side_lengths[1] * side_lengths[2]
+        ) / (4.0 * area)
+
+        if circumradius < 1.0 / alpha:
+            kept.append(tri)
+
+    if not kept:
+        return MultiPoint(points).convex_hull
+
+    return unary_union(kept)
+
+
+def generate_tissue_boundary(
+    cells_df,
+    x_col="x_centroid",
+    y_col="y_centroid",
+    method="alpha_shape",
+    alpha=0.05,
+    simplify_tolerance=None,
+    output_csv=None,
+):
+    """
+    Generate a tissue boundary polygon from cell spatial coordinates.
+
+    Parameters
+    ----------
+    cells_df : pandas.DataFrame
+        Cell-level table containing spatial coordinates.
+    x_col, y_col : str
+        Column names for x and y coordinates.
+    method : {"alpha_shape", "convex_hull"}
+        Geometry method for boundary estimation.
+    alpha : float
+        Alpha parameter for alpha-shape.
+    simplify_tolerance : float or None
+        Optional polygon simplification tolerance.
+    output_csv : str or Path or None
+        If provided, write boundary to CSV.
+
+    Returns
+    -------
+    pandas.DataFrame
+        Columns: ["x", "y", "order"]
+    """
+    if x_col not in cells_df or y_col not in cells_df:
+        raise ValueError(
+            f"cells_df must contain columns '{x_col}' and '{y_col}'"
+        )
+
+    points = (
+        cells_df[[x_col, y_col]]
+        .dropna()
+        .to_numpy()
+    )
+
+    if len(points) == 0:
+        raise ValueError("No valid spatial coordinates found.")
+
+    if method == "convex_hull":
+        polygon = MultiPoint(points).convex_hull
+    elif method == "alpha_shape":
+        polygon = _alpha_shape(points, alpha=alpha)
+    else:
+        raise ValueError(f"Unknown method: {method}")
+
+    if simplify_tolerance is not None:
+        polygon = polygon.simplify(simplify_tolerance)
+
+    # ------------------------------------------------------------------
+    # Normalize geometry:
+    # tissue boundary must be a single outer polygon
+    # (consistent with tissueboundary.txt behavior)
+    # ------------------------------------------------------------------
+    if isinstance(polygon, MultiPolygon):
+        polygon = max(polygon.geoms, key=lambda p: p.area)
+
+    if not isinstance(polygon, Polygon):
+        raise TypeError(
+            f"Expected Polygon after processing, got {type(polygon)}"
+        )
+
+    x, y = polygon.exterior.coords.xy
+
+    boundary_df = pd.DataFrame({
+        "x": x,
+        "y": y,
+        "order": np.arange(len(x)),
+    })
+
+    if output_csv is not None:
+        boundary_df.to_csv(output_csv, index=False)
+
+    return boundary_df

{histoseg-0.1.7.dist-info → histoseg-0.1.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: histoseg
-Version: 0.1.7
+Version: 0.1.8.1
 Summary: ...
 Author-email: Taobo Hu <taobo.hu@scilifelab.se>
 License: Required Notice: Copyright (c) 2025 SPATHO AB.
@@ -86,7 +86,6 @@ Project-URL: Documentation, https://histoseg.readthedocs.io
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-License-File: AUTHORS.rst
 Dynamic: license-file
 
 <div align="center">

{histoseg-0.1.7.dist-info → histoseg-0.1.8.1.dist-info}/RECORD

@@ -1,15 +1,16 @@
 histoseg/__init__.py,sha256=ssVwpgspXb7TWi1aAbWYA82FBJhGZH1g-JIvosVocTM,982
-histoseg/_version.py,sha256=szvPIs2C82UunpzuvVg3MbF4QhzbBYTsVJ8DmPfq6_E,704
+histoseg/_version.py,sha256=DceX3WwB1oE06QTAMXFaSlGTc9twNCVWkTErPbrlF7o,709
 histoseg/contours/__init__.py,sha256=8YEy98MnGOhJg1BHkVZ_qPtTYUWPoIDAOT60F5EfHgY,32
 histoseg/contours/pattern1_isoline.py,sha256=6JVL26O7AZ0s0YyloDoiUdIHTJ7jp6gEooFWnMoNhSw,19592
+histoseg/geometry/__init__.py,sha256=5Aep5GBj2u4k2415QIECd0vK3y2eVBfQZRIskOgzb78,101
+histoseg/geometry/tissue_boundary.py,sha256=-12lyNYI93JkNlBDT_Fv7SLAeTLKMZ9fPhqpSTowFz0,3680
 histoseg/gui/__init__.py,sha256=SJvM-gRCwQ0X7fufPmdNO43X3wQvlnFHFmFNswt1hlw,133
 histoseg/gui/gui_app.py,sha256=copFjJzMEeg2T4HV4--KHq9GG-v58xeW-eqRQ0-uJww,15259
 histoseg/io/__init__.py,sha256=kH_F15ApTutYbEUGAkV9QxBv8Ho863xvWK0mRmKeOCA,27
 histoseg/io/huggingface.py,sha256=YL_aXAXiHMMk6T6bqX-zPXFFChO83CVhTxI6mX52Z7g,2124
 histoseg/sfplot/Searcher_Findee_Score.py,sha256=Y9UzWrqap029BOyOnFPklvK4v-2wm3r_PkmUh65DEqo,14951
-histoseg-0.1.7.dist-info/licenses/AUTHORS.rst,sha256=T3nRBgyOUCoWU3rxF4Iy_tdd-1kJjyLBfdBwEQQswyw,202
-histoseg-0.1.7.dist-info/licenses/LICENSE,sha256=z7Ztufk460DPfU3rgZEstjCQK3EbwHbD4JSmF_7y0qA,4764
-histoseg-0.1.7.dist-info/METADATA,sha256=UZ-r82SGkB8uG1UoAAUsLshObJzESpdUkx8QAB2KbXI,13216
-histoseg-0.1.7.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-histoseg-0.1.7.dist-info/top_level.txt,sha256=dvphnIeqaZamvJULm-I5qztYoGO8WLLCY85z0xrXsb0,9
-histoseg-0.1.7.dist-info/RECORD,,
+histoseg-0.1.8.1.dist-info/licenses/LICENSE,sha256=z7Ztufk460DPfU3rgZEstjCQK3EbwHbD4JSmF_7y0qA,4764
+histoseg-0.1.8.1.dist-info/METADATA,sha256=LQR8kK-wQSM9bqc_8WM0SUmYXYGrsaoHB5_GBFeECSg,13192
+histoseg-0.1.8.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+histoseg-0.1.8.1.dist-info/top_level.txt,sha256=dvphnIeqaZamvJULm-I5qztYoGO8WLLCY85z0xrXsb0,9
+histoseg-0.1.8.1.dist-info/RECORD,,

histoseg-0.1.7.dist-info/licenses/AUTHORS.rst

@@ -1,14 +0,0 @@
-=======
-Credits
-=======
-
-Development Lead
-----------------
-
-* Taobo Hu <taobo.hu@scilifelab.se>
-* Mengping Long <mengping.long@scilifelab.se>
-
-Contributors
-------------
-
-None yet. Why not be the first?