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Load visium as SPE #16

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Merged
keviny2 merged 11 commits into from
Feb 28, 2025
Merged

Load visium as SPE #16

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43e4930
WIP: Implement read_10x_visium
keviny2 Feb 4, 2025
d0ce816
WIP: Wait for combine ops on SpatialExperiment objs to be implemented
keviny2 Feb 17, 2025
bee220c
Merge branch 'main' into visium
keviny2 Feb 26, 2025
de4132b
read_tenx_visium executes successfully
keviny2 Feb 27, 2025
8582691
Initial test for read_tenx_visium passing
keviny2 Feb 27, 2025
f75cbf3
Restrict scipy version to be compatible with python>=3.9
keviny2 Feb 27, 2025
1eab875
WIP: Working on last test case for read_tenx_visium
keviny2 Feb 27, 2025
d9495c5
Fix test_tissue_positions_files test case
keviny2 Feb 28, 2025
4b1977b
Update CHANGELOG
keviny2 Feb 28, 2025
0b903b2
Handle paths and urls more reliably
keviny2 Feb 28, 2025
b21d90d
Localize dependencies
keviny2 Feb 28, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# Changelog

## Version 0.0.6
- Added `read_tenx_visium()` function to load 10x Visium data as SpatialExperiment
- Added `combine_columns` function
- Implemented `__eq__` override for `SpatialImage` subclasses

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8 changes: 6 additions & 2 deletions setup.cfg
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Expand Up @@ -52,9 +52,9 @@ install_requires =
biocframe>=0.6.1
biocutils>=0.2
summarizedexperiment>=0.5
singlecellexperiment>=0.5.6
singlecellexperiment>=0.5.7
pillow>=11.0
requests
scipy~=1.13
geopandas


Expand All @@ -67,12 +67,16 @@ exclude =
# Add here additional requirements for extra features, to install with:
# `pip install SpatialExperiment[PDF]` like:
# PDF = ReportLab; RXP
optional =
pandas
requests

# Add here test requirements (semicolon/line-separated)
testing =
setuptools
pytest
pytest-cov
%(optional)s
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@jkanche jkanche Mar 1, 2025

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This is cool, wish i knew we can do this


[options.entry_points]
# Add here console scripts like:
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13 changes: 13 additions & 0 deletions src/spatialexperiment/__init__.py
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Expand Up @@ -16,6 +16,7 @@
del version, PackageNotFoundError

from .ProxySFE import ProxySpatialFeatureExperiment
from .io import read_tenx_visium
from .SpatialExperiment import SpatialExperiment
from .SpatialImage import (
LoadedSpatialImage,
Expand All @@ -24,3 +25,15 @@
VirtualSpatialImage,
construct_spatial_image_class,
)

__all__ = [
"ProxySpatialFeatureExperiment",
"read_tenx_visium",
"SpatialExperiment",
"LoadedSpatialImage",
"RemoteSpatialImage",
"StoredSpatialImage",
"VirtualSpatialImage",
"construct_spatial_image_class",
]

83 changes: 82 additions & 1 deletion src/spatialexperiment/_imgutils.py
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@@ -1,12 +1,91 @@
from typing import Union

import os
from io import BytesIO
from pathlib import Path
from urllib.parse import urlparse
from PIL import Image
from biocframe import BiocFrame
from .SpatialImage import construct_spatial_image_class

__author__ = "keviny2"
__copyright__ = "keviny2"
__license__ = "MIT"



def read_image(input_image):
"""Read image from PIL Image, file path, or URL.

Args:
input_image: PIL Image, string path to local file, or URL string.

Returns:
The loaded image.

Raises:
TypeError: If input is not PIL Image, path string, or URL string.
"""
import requests

if isinstance(input_image, Image.Image):
return input_image

if isinstance(input_image, (str, Path)):
is_url = urlparse(str(input_image)).scheme in ("http", "https", "ftp")
if is_url:
response = requests.get(input_image)
return Image.open(BytesIO(response.content))
else:
return Image.open(input_image)

raise TypeError(f"Expected PIL Image, path, or URL. Got {type(input_image)}")


def get_img_data(
img: Union[str, os.PathLike],
scale_factor: str,
sample_id: str,
image_id: str,
load: bool = True
) -> BiocFrame:
"""
Construct an image data dataframe.

Args:
img:
A path or url to the image file.

scale_factor:
The scale factor associated with the image.

sample_id:
A unique identifier for the sample to which the image belongs.

image_id:
A unique identifier for the image itself.

load:
A boolean specifying whether the image(s) should be loaded into memory? If False, will store the path/URL instead.
Defaults to `True`.

Returns:
The image data.
"""
if load:
img = read_image(img)

spi = construct_spatial_image_class(img)
return BiocFrame(
{
"sample_id": [sample_id],
"image_id": [image_id],
"data": [spi],
"scale_factor": [scale_factor]
}
)


def retrieve_rows_by_id(
img_data: BiocFrame,
sample_id: Union[str, bool, None] = None,
Expand All @@ -16,7 +95,9 @@ def retrieve_rows_by_id(
Retrieve rows from `img_data` based on specified `sample_id` and `image_id`.

Args:
img_data: The data from which to retrieve rows.
img_data:
The data from which to retrieve rows.

sample_id:
- `sample_id=True`: Matches all samples.
- `sample_id=None`: Matches the first sample.
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4 changes: 2 additions & 2 deletions src/spatialexperiment/_initutils.py
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Expand Up @@ -3,7 +3,7 @@

from biocframe import BiocFrame
from PIL import Image
from SpatialImage import SpatialImage
from .SpatialImage import construct_spatial_image_class
from summarizedexperiment._frameutils import _sanitize_frame

__author__ = "keviny2"
Expand Down Expand Up @@ -96,7 +96,7 @@ def construct_img_data(
spis = []
for image_source in image_sources:
result = Image.open(image_source) if load_image else image_source
spi = SpatialImage(result)
spi = construct_spatial_image_class(result)
spis.append(spi)

img_data = {
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4 changes: 4 additions & 0 deletions src/spatialexperiment/io/__init__.py
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@@ -0,0 +1,4 @@
from .tenx_visium import read_tenx_visium

__all__ = ["read_tenx_visium"]

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