Merge pull request #135 from saeyslab/SC_20_issue_irregular_chunking

SC_20 fix chunk issue transcripts + upgrade packag
saeyslab · Sep 6, 2023 · 641fc92 · 641fc92
2 parents 0f7945c + d7acae0
commit 641fc92
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/environment.yml b/environment.yml
@@ -5,31 +5,29 @@ channels:
 dependencies:
  - geopandas=0.12.2
  - leidenalg=0.9.1
- - matplotlib=3.5.2
  - napari=0.4.16
- - numpy=1.24.4
  - opencv=4.5.5
  - pip=22.2.2
  - python=3.10.8
  - pytorch=1.12.1
  - rasterio=1.3.2
- - scanpy=1.9.1
+ - scanpy=1.9.4
  - scipy=1.8.0
  - seaborn=0.11.2
  - fsspec=2023.6.0
  - pip:
- - anndata==0.9.1
+ - anndata==0.9.2
  - basicpy==1.0.0
  - cellpose==2.0.5
  - jax==0.4.6
  - jaxlib==0.4.6
  - shapely==2.0.1
- - spatialdata==0.0.9
+ - spatialdata==0.0.12
  - squidpy==1.2.0
  - voronoi-diagram-for-polygons==0.1.6
  - xarray==2022.12.0
  - xarray-dataclasses==1.5.0
  - xarray-datatree==0.0.12
  - xarray-schema==0.0.3
  - xarray-spatial==0.3.5
- - pandas==1.4.2
+ - pandas==1.4.3
diff --git a/setup.cfg b/setup.cfg
@@ -30,12 +30,12 @@ project_urls =
 [options]
 packages = find:
 install_requires =
- pandas==1.4.2
- spatialdata==0.0.9
+ pandas==1.4.3,
+ spatialdata>=0.0.9
  cellpose==2.0.5
  squidpy==1.2.0
- matplotlib<3.7 # scanpy not compatible with matplotlib>=3.7
- scanpy==1.9.1
+ #matplotlib<3.7 # scanpy not compatible with matplotlib>=3.7
+ scanpy>=1.9.1
  jax==0.4.6
  jaxlib==0.4.6
  basicpy==1.0.0

diff --git a/src/napari_sparrow/image/_transcripts.py b/src/napari_sparrow/image/_transcripts.py
@@ -166,6 +166,8 @@ def chunked_gaussian_filter(chunk):
  )
 
  blurred_transcripts = blurred_transcripts.T
+ # rechunk, otherwise possible issues when saving to zarr
+ blurred_transcripts=blurred_transcripts.rechunk( blurred_transcripts.chunksize )
 
  spatial_image = spatialdata.models.Image2DModel.parse(
  blurred_transcripts[None,], dims=("c", "y", "x")