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Merged
newmana merged 12 commits into from
Jun 16, 2026
Merged

Fix data type errors #352

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4326694
Remove dead code and start to tidy up types.
newmana Jun 16, 2026
739d89a
Start to tidy up types, fix old calls to AgglomerativeClustering.
newmana Jun 16, 2026
f1a4142
Start to tidy up types.
newmana Jun 16, 2026
4359496
Start to tidy up types and remove old code.
newmana Jun 16, 2026
3d9494f
Start to tidy up types.
newmana Jun 16, 2026
55e2cd3
Fix formatting and type.
newmana Jun 16, 2026
6554e73
Fix up types, docstring and add tests for issues #350 and #300.
newmana Jun 16, 2026
5b93cdc
Upgrade to 1.4.1.
newmana Jun 16, 2026
718be6e
Upgrade pillow.
newmana Jun 16, 2026
d67f17f
More data type fixes and improve speed of generating random pairs.
newmana Jun 16, 2026
b45a467
Document change.
newmana Jun 16, 2026
8756251
Fix formatting.
newmana Jun 16, 2026
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9 changes: 9 additions & 0 deletions HISTORY.rst
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down
2 changes: 2 additions & 0 deletions docs/index.rst
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down
11 changes: 11 additions & 0 deletions docs/release_notes/1.4.1.rst
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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0
2 changes: 2 additions & 0 deletions docs/release_notes/index.rst
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Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
{ name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
"leidenalg>=0.11.0",
"numba>=0.58.1",
"numpy>=2.4.0",
"pillow>=11.0.0,<12.0",
"pillow>=12.0.0,<13.0",
"scanpy>=1.12.0",
"scikit-image>=0.22.0",
"pandas>=2.3.0",
Expand Down
2 changes: 1 addition & 1 deletion stlearn/__init__.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down
36 changes: 24 additions & 12 deletions stlearn/adds/add_mask.py
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
library_id = next(iter(adata.uns["spatial"].keys()))
quality = adata.uns["spatial"][library_id]["use_quality"]
except Exception as e:
raise KeyError("""\
raise KeyError(
"""\
Please read ST data first and try again
""") from e
"""
) from e

if imgpath is not None and os.path.isfile(imgpath):
try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
adata.uns["mask_image"][library_id][key][quality] = img
print("Added tissue mask to the object!")
except Exception as e:
raise ValueError(f"""\
raise ValueError(
f"""\
{imgpath!r} does not end on a valid extension.
""") from e
"""
) from e
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{imgpath!r} does not end on a valid extension.
""")
"""
)
return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
library_id = next(iter(adata.uns["spatial"].keys()))
quality = adata.uns["spatial"][library_id]["use_quality"]
except Exception as e:
raise KeyError("""\
raise KeyError(
"""\
Please read ST data first and try again
""") from e
"""
) from e

if masks == "all":
masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
try:
mask_image = adata.uns["mask_image"][library_id][mask][quality]
except Exception as e:
raise KeyError(f"""\
raise KeyError(
f"""\
Please load mask {mask} images first and try again
""") from e
"""
) from e

# Normalise to uint8 if the image is float in [0, 1]
if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
elif select == "white":
mask_image = np.where(mask_image >= 155, 1, 0)
else:
raise ValueError("""\
raise ValueError(
"""\
Only support black and white mask yet.
""")
"""
)
mask_image_2d = mask_image.mean(axis=2)

def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down
12 changes: 8 additions & 4 deletions stlearn/adds/image.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

print("Added tissue image to the object!")
except Exception as e:
raise ValueError(f"""\
raise ValueError(
f"""\
{imgpath!r} does not end on a valid extension.
""") from e
"""
) from e
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{imgpath!r} does not end on a valid extension.
""")
"""
)
return adata if copy else None
6 changes: 4 additions & 2 deletions stlearn/spatial/sme/_weighting_matrix.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
array_col = adata.obs_names.map(lambda x: x.split("x")[0])
rate = 1.5
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{platform!r} does not support.
""")
"""
)
regression = LinearRegression()
reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down
6 changes: 4 additions & 2 deletions stlearn/spatial/sme/pseudo_spot.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
).reset_index()
obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{platform!r} does not support.
""")
"""
)

reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down
6 changes: 4 additions & 2 deletions stlearn/spatial/sme/sme_impute0.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
elif isinstance(adata.X, pd.Dataframe):
count_embed = adata.X.values
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{type(adata.X)} is not a valid type.
""")
"""
)
else:
count_embed = adata.obsm[use_data]

Expand Down
6 changes: 4 additions & 2 deletions stlearn/spatial/sme/sme_normalize.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
elif isinstance(adata.X, pd.Dataframe):
count_embed = adata.X.values
else:
raise ValueError(f"""\
raise ValueError(
f"""\
{type(adata.X)} is not a valid type.
""")
"""
)
else:
count_embed = adata.obsm[use_data]

Expand Down
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Fix data type errors#352

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 Merged

newmana
merged 12 commits into

from

Jun 16, 2026
 Merged


Fix data type errors
#352
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4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Fix data type errors#352

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

newmana
merged 12 commits into

from

Jun 16, 2026
 Merged


Fix data type errors
#352
Show file tree
Hide file tree
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Commits

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12 commits


Select commit
Hold shift + click to select a range
4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
Loading

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// Highlight search terms from Google/DuckDuckGo/Bing referrer
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var ref = document.referrer;
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span.className = 'userscript-highlight';
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Fix data type errors#352

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 Merged

newmana
merged 12 commits into

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Jun 16, 2026
 Merged


Fix data type errors
#352
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4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
Loading

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// Strip utm_, fbclid, gclid, etc. from all links on page
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var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Fix data type errors#352

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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 Merged

newmana
merged 12 commits into

from

Jun 16, 2026
 Merged


Fix data type errors
#352
Show file tree
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12 commits


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Hold shift + click to select a range
4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
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Fix data type errors#352

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 Merged

newmana
merged 12 commits into

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Jun 16, 2026
 Merged


Fix data type errors
#352
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4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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HISTORY.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Fix data type errors#352

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

newmana
merged 12 commits into

from

Jun 16, 2026
 Merged


Fix data type errors
#352
Show file tree
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Commits

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12 commits


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4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
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var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
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document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
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if (enabled && !document.getElementById('universal-dark-mode-style')) {
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
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Fix data type errors by newmana · Pull Request #352 · BiomedicalMachineLearning/stLearn · GitHub
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 Merged

newmana
merged 12 commits into

from

Jun 16, 2026
 Merged


Fix data type errors
#352
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4326694

Remove dead code and start to tidy up types.


newmana Jun 16, 2026
739d89a

Start to tidy up types, fix old calls to AgglomerativeClustering.


newmana Jun 16, 2026
f1a4142

Start to tidy up types.


newmana Jun 16, 2026
4359496

Start to tidy up types and remove old code.


newmana Jun 16, 2026
3d9494f

Start to tidy up types.


newmana Jun 16, 2026
55e2cd3

Fix formatting and type.


newmana Jun 16, 2026
6554e73

Fix up types, docstring and add tests for issues #350 and #300.


newmana Jun 16, 2026
5b93cdc

Upgrade to 1.4.1.


newmana Jun 16, 2026
718be6e

Upgrade pillow.


newmana Jun 16, 2026
d67f17f

More data type fixes and improve speed of generating random pairs.


newmana Jun 16, 2026
b45a467

Document change.


newmana Jun 16, 2026
8756251

Fix formatting.


newmana Jun 16, 2026

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9 changes: 9 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,6 +2,15 @@
History
=======

1.4.1 (2026-06-16)
------------------
* Improved speed of random spot generation used in permutation testing.

API and Bug Fixes:
* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

1.4.0 (2026-05-01)
------------------
* Removed tensorflow and keras and replaced with torch and torchvision.
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,6 +38,8 @@ undissociated tissue sample.
Latest Additions
----------------

.. include:: release_notes/1.4.1.rst

.. include:: release_notes/1.4.0.rst

.. include:: release_notes/1.3.0.rst
Expand Down

11 changes: 11 additions & 0 deletions
docs/release_notes/1.4.1.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1.4.1 `2026-06-16`
~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features
* Improved speed of random spot generation used in permutation testing.

.. rubric:: Bugs

* Fixed up docstring and types for various CCI methods.
* Fixes for issues #350 and #300 with incorrect types.
* Upgrade libraries: pillow>=12.0.0,<13.0

2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.4.1.rst

.. include:: 1.4.0.rst

.. include:: 1.3.0.rst
Expand Down

4 changes: 2 additions & 2 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "stlearn"
version = "1.4.0"
version = "1.4.1"
authors = [
 { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
]
Expand All@@ -20,7 +20,7 @@ dependencies = [
 "leidenalg>=0.11.0",
 "numba>=0.58.1",
 "numpy>=2.4.0",
 "pillow>=11.0.0,<12.0",
 "pillow>=12.0.0,<13.0",
 "scanpy>=1.12.0",
 "scikit-image>=0.22.0",
 "pandas>=2.3.0",
Expand Down

2 changes: 1 addition & 1 deletion
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@

__author__ = """Genomics and Machine Learning Lab"""
__email__ = "andrew.newman@uq.edu.au"
__version__ = "1.4.0"
__version__ = "1.4.1"

from . import add, datasets, em, pl, pp, spatial, tl, types
from ._settings import settings
Expand Down

36 changes: 24 additions & 12 deletions
stlearn/adds/add_mask.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,9 +38,11 @@ def add_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if imgpath is not None and os.path.isfile(imgpath):
 try:
Expand All@@ -59,13 +61,17 @@ def add_mask(
 adata.uns["mask_image"][library_id][key][quality] = img
 print("Added tissue mask to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None


Expand DownExpand Up@@ -128,9 +134,11 @@ def apply_mask(
 library_id = next(iter(adata.uns["spatial"].keys()))
 quality = adata.uns["spatial"][library_id]["use_quality"]
 except Exception as e:
 raise KeyError("""\
 raise KeyError(
 """\
 Please read ST data first and try again
 """) from e
 """
 ) from e

 if masks == "all":
 masks = list(adata.uns["mask_image"][library_id].keys())
Expand All@@ -144,9 +152,11 @@ def apply_mask(
 try:
 mask_image = adata.uns["mask_image"][library_id][mask][quality]
 except Exception as e:
 raise KeyError(f"""\
 raise KeyError(
 f"""\
 Please load mask {mask} images first and try again
 """) from e
 """
 ) from e

 # Normalise to uint8 if the image is float in [0, 1]
 if mask_image.dtype.kind == "f" and mask_image.max() <= 1.0:
Expand All@@ -157,9 +167,11 @@ def apply_mask(
 elif select == "white":
 mask_image = np.where(mask_image >= 155, 1, 0)
 else:
 raise ValueError("""\
 raise ValueError(
 """\
 Only support black and white mask yet.
 """)
 """
 )
 mask_image_2d = mask_image.mean(axis=2)

 def apply_spot_mask(x, _mask=mask, _i=i, _mask_image_2d=mask_image_2d):
Expand Down

12 changes: 8 additions & 4 deletions
stlearn/adds/image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -71,11 +71,15 @@ def image(

 print("Added tissue image to the object!")
 except Exception as e:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """) from e
 """
 ) from e
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {imgpath!r} does not end on a valid extension.
 """)
 """
 )
 return adata if copy else None

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/_weighting_matrix.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -36,9 +36,11 @@ def row_col_by_platform(
 array_col = adata.obs_names.map(lambda x: x.split("x")[0])
 rate = 1.5
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )
 regression = LinearRegression()
 reg_row: LinearRegression = regression.fit(array_row.values.reshape(-1, 1), img_row) # type: ignore
 reg_col: LinearRegression = regression.fit(array_col.values.reshape(-1, 1), img_col) # type: ignore
Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/pseudo_spot.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -172,9 +172,11 @@ def pseudo_spot(
 ).reset_index()
 obs_df.drop_duplicates(subset=["array_row", "array_col"], keep="last")
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {platform!r} does not support.
 """)
 """
 )

 reg_row = LinearRegression().fit(array_row.values.reshape(-1, 1), img_row)

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_impute0.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_impute0(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down

6 changes: 4 additions & 2 deletions
stlearn/spatial/sme/sme_normalize.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -61,9 +61,11 @@ def sme_normalize(
 elif isinstance(adata.X, pd.Dataframe):
 count_embed = adata.X.values
 else:
 raise ValueError(f"""\
 raise ValueError(
 f"""\
 {type(adata.X)} is not a valid type.
 """)
 """
 )
 else:
 count_embed = adata.obsm[use_data]

Expand Down
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