minor fixes

Author: quentinblampey

CHANGELOG.md

@@ -5,12 +5,14 @@
 - Can provide `qv_threshold` argument to the Xenium reader to filter low quality transcripts @callum-jpg (#210)
 
 ### Changed
-- Storing patches embeddings as an `AnnData` object instead of images (#212)
+- Storing patches embeddings as an `AnnData` object instead of images (#212) (see [updated tuto](https://gustaveroussy.github.io/sopa/tutorials/he/))
 
 ### Fixed
 - Right sorting scales for WSI reader with openslide backend @stergioc (#209)
 - When a polygon cannot be simplified (for the Xenium Explorer), convert it to a circle (#206)
 - `sopa explorer write`: use correct default argument for `table_key` in the CLI (#211)
+- Fix Baysor usage on Windows (#185)
+- Fix tight patches returning a different number of patches (#214)
 
 ## [2.0.1] - 2025-02-10
 

sopa/_constants.py

@@ -68,5 +68,4 @@ class SopaFiles:
 
 VALID_DIMENSIONS = ("c", "y", "x")
 LOW_AVERAGE_COUNT = 0.01
-EPS = 1e-5
 ATTRS_KEY = "spatialdata_attrs"

sopa/patches/_patches.py

@@ -11,7 +11,7 @@
 from spatialdata.transformations import get_transformation
 from xarray import DataArray, DataTree
 
-from .._constants import EPS, SopaKeys
+from .._constants import SopaKeys
 from ..utils import add_spatial_element, to_intrinsic
 
 log = logging.getLogger(__name__)
@@ -44,7 +44,7 @@ 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 + EPS
+        return ceil(width) if self.int_coords else width + 1e-4  # add an epsilon to avoid floating point errors (#214)
 
     def __getitem__(self, i):
         start_delta = i * (self.patch_width - self.patch_overlap)

tests/test_patches.py

@@ -1,9 +1,11 @@
+import numpy as np
 import pandas as pd
 import pytest
 from spatialdata import SpatialData
 
 import sopa
 from sopa._constants import SopaFiles, SopaKeys
+from sopa.patches._patches import Patches1D
 
 
 @pytest.fixture
@@ -32,6 +34,15 @@ def test_patchify_inside_tissue_roi(sdata: SpatialData):
     del sdata.shapes[SopaKeys.ROI]
 
 
+def test_pathify_transcripts():
+    # reproduce issue #214
+
+    xmax = np.float32(11475.797)
+    xmin = np.float32(2.671875)
+
+    Patches1D(xmin=xmin, xmax=xmax, patch_width=300.0, patch_overlap=30.0, tight=True, int_coords=False)
+
+
 def test_patchify_baysor(sdata: SpatialData):
     with pytest.raises(AssertionError):
         sopa.utils.get_transcripts_patches_dirs(sdata)