fix baysor tight layout #23

CHANGELOG.md

@@ -12,6 +12,9 @@
 - The `uniform` toy dataset now has two coordinate systems (better test case)
 - Faster table conversion to the Xenium Explorer
 
+### Fixed
+- Tight patching more stable with epsilon constant
+
 ## [1.0.2] - 2024-01-15
 
 ### Fix

sopa/_constants.py

@@ -28,6 +28,7 @@ class SopaKeys:
 
 VALID_DIMENSIONS = ("c", "y", "x")
 LOW_AVERAGE_COUNT = 0.01
+EPS = 1e-5
 
 
 class ROI:

sopa/segmentation/patching.py

@@ -14,7 +14,7 @@
 from spatialdata.models import ShapesModel
 from spatialdata.transformations import get_transformation
 
-from .._constants import ROI, SopaFiles, SopaKeys
+from .._constants import EPS, ROI, SopaFiles, SopaKeys
 from .._sdata import get_boundaries, get_item, get_spatial_image, to_intrinsic
 
 log = logging.getLogger(__name__)
@@ -32,7 +32,9 @@ def __init__(self, xmin, xmax, patch_width, patch_overlap, tight, int_coords):
         self._count = self.count()
         if tight:
             self.patch_width = self.tight_width()
-            assert self._count == self.count()
+            assert (
+                self._count == self.count()
+            ), f"Invalid patching with {self.delta=}, {self.patch_width=} and {self.patch_overlap=}"
 
     def count(self):
         if self.patch_width >= self.delta:
@@ -45,7 +47,7 @@ def update(self, patch_width):
 
     def tight_width(self):
         width = (self.delta + (self._count - 1) * self.patch_overlap) / self._count
-        return ceil(width) if self.int_coords else width
+        return ceil(width) if self.int_coords else width + EPS
 
     def __getitem__(self, i):
         start_delta = i * (self.patch_width - self.patch_overlap)

tests/test_patches.py

@@ -34,10 +34,10 @@ def _patchify_transcripts(sdata: SpatialData, width: int, overlap: int) -> list[
 
 
 def test_patchify_baysor(sdata: SpatialData):
-    valid_indices = _patchify_transcripts(sdata, 300, 100)
+    valid_indices = _patchify_transcripts(sdata, 30, 10)
     assert len(valid_indices) == 9
 
-    valid_indices = _patchify_transcripts(sdata, 512, 0)
+    valid_indices = _patchify_transcripts(sdata, 52, 0)
     assert len(valid_indices) == 1