Add tutorial roi regions by sophiamaedler · Pull Request #330 · MannLabs/scPortrait

sophiamaedler · 2025-11-06T15:55:07Z

Aim of this PR is to add a tutorial that shows how you can annotate regions in scPortrait. It will implement additonal functions required to streamline this functionality.

New Features:

update adata.obs to disk
add plotting support for non memory backed h5sc files
add functions to subset h5sc objects according to cell_id (a new h5sc is written to disk)
improve h5sc tests

Bug Fixes:

correctly read dimensions to generate a new axes object when plotting a spatialdata shapes layer

Keeps track of filepath in uns from which the h5sc object was loaded. This allows you to update values (e.g. obs) on disk.

…ensions from shape file

Add function to mask tissue regions

doesn't yet cover all functions

sophiamaedler · 2025-11-17T22:49:38Z

scPortrait_demo_annotate_regions.ipynb

current tutorial covering the newly implemented functions

for more information, see https://pre-commit.ci

Copilot

Pull request overview

This PR adds functionality for annotating and subsetting regions in scPortrait, along with improvements to h5sc file handling and testing.

Changes:

Added functions to mask/crop images using spatial regions and subset h5sc objects by cell IDs
Enhanced h5sc operations to support updating obs data on disk and adding spatial coordinates
Improved plotting support for non-memory-backed h5sc files and fixed spatial coordinate handling
Expanded test coverage for subset operations and h5sc plotting functionality

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/unit_tests/tools/sdata/test_subset.py	New comprehensive tests for spatial region masking and bounding box subsetting
tests/unit_tests/tools/h5sc/test_operations.py	New tests for h5sc subsetting and disk operations
tests/unit_tests/plotting/test_h5sc.py	Refactored to use real h5sc fixtures instead of mocks
tests/conftest.py	Added spatial data fixtures for testing region selection
src/scportrait/tools/sdata/processing/_subset.py	Implemented mask_region function for spatial masking/cropping
src/scportrait/tools/sdata/processing/init.py	Exported new mask_region function
src/scportrait/tools/h5sc/operations.py	Added functions for updating obs on disk, spatial coordinates, and cell subsetting
src/scportrait/tools/h5sc/init.py	Exported new h5sc operation functions
src/scportrait/plotting/sdata.py	Fixed dimension calculation for GeoDataFrame shapes
src/scportrait/plotting/h5sc.py	Added support for non-memory-backed h5sc plotting
src/scportrait/pipeline/project.py	Improved h5sc handle management to prevent file handle leaks
src/scportrait/pipeline/mask_filtering/region_masking.py	New module for image masking with automatic region detection
src/scportrait/pipeline/_utils/spatialdata_helper.py	Added debug print statement for memory calculation
src/scportrait/pipeline/_utils/constants.py	Added DEFAULT_IDENTIFIER_FILENAME constant
src/scportrait/io/h5sc.py	Updated to store file handle and source path in uns
requirements/requirements.txt	Added affine and rasterio dependencies
src/scportrait/tools/sdata/write/_write.py	Fixed channel name comparison logic

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Copilot · 2026-02-05T10:39:46Z

src/scportrait/tools/sdata/processing/_subset.py

+    elif isinstance(image, xr.DataArray):
+        image = image
+
+    print(image.dtype)


Debug print statement should be removed before merging to production. If this information is needed for diagnostics, consider using proper logging instead.

Copilot · 2026-02-05T10:39:46Z

src/scportrait/pipeline/_utils/spatialdata_helper.py

    transform = get_transformation(mask, coordinate_system)

    if check_memory(mask):
+        print("Array fits in memory, using in-memory calculation.")


Debug print statement should be removed or replaced with proper logging. For production code, use the logging module to allow users to control output verbosity.

Copilot · 2026-02-05T10:39:47Z

src/scportrait/plotting/h5sc.py

+    else:
+        # non backed h5sc adata objects can be accessed directly
+        # these are created by slicing original h5sc objects
+        col = "scportrait_cell_id"


The hardcoded column name 'scportrait_cell_id' is duplicated here and in lines 393-394. Consider importing and using DEFAULT_CELL_ID_NAME constant from scportrait.pipeline._utils.constants to maintain consistency.

Suggested change

col = "scportrait_cell_id"

col = DEFAULT_CELL_ID_NAME

Copilot · 2026-02-05T10:39:47Z

src/scportrait/tools/h5sc/operations.py

+        If `to_disk` is False, returns the subsetted AnnData object. If `to_disk` is True, saves the subsetted AnnData object to disk and returns None.
+    """
+    if outpath is not None:
+        if not isinstance(outpath, (str | Path)):


The isinstance check should use a tuple syntax for multiple types: isinstance(outpath, (str, Path)) instead of (str | Path). The union operator syntax is only valid in type hints, not in runtime isinstance checks.

Suggested change

if not isinstance(outpath, (str | Path)):

if not isinstance(outpath, (str, Path)):

Copilot · 2026-02-05T10:39:47Z

src/scportrait/pipeline/project.py

+        # Load a fresh AnnData
+        adata = read_h5sc(self.extraction_f.output_path or self.extraction_f.extraction_file)


This will fail if extraction_f is None (as checked in the old code). The validation should still be performed before attempting to read the h5sc file, otherwise this will raise an AttributeError.

Suggested change

# Load a fresh AnnData

adata = read_h5sc(self.extraction_f.output_path or self.extraction_f.extraction_file)

# Ensure extraction configuration is available before accessing its attributes

extraction_f = getattr(self, "extraction_f", None)

if extraction_f is None:

raise ValueError(

"Extraction configuration 'extraction_f' is not set. "

"Run the extraction step before accessing 'h5sc'."

)

# Load a fresh AnnData

adata = read_h5sc(extraction_f.output_path or extraction_f.extraction_file)

Copilot · 2026-02-05T10:39:48Z

src/scportrait/tools/sdata/write/_write.py

                    )
                channel_names_old = image.coords["c"].values.tolist()
-                if channel_names_old != channel_names:
+                if any(channel_names_old != channel_names):


The comparison channel_names_old != channel_names produces a boolean array when comparing lists/arrays element-wise. The correct check should be channel_names_old != channel_names (direct list comparison) or not np.array_equal(channel_names_old, channel_names) if they are numpy arrays. Using any() on a scalar boolean will fail if they are plain lists.

Suggested change

if any(channel_names_old != channel_names):

if channel_names_old != channel_names:

Laurens Lehner and others added 17 commits November 12, 2024 00:07

Add draft function to mask tissue regions

4ba2ff8

[FEATURE] store filepath when reading h5sc files

8b224eb

Keeps track of filepath in uns from which the h5sc object was loaded. This allows you to update values (e.g. obs) on disk.

[FIX] if no axes object is provided to plot_shapes correctly read dim…

33ff5b3

…ensions from shape file

add functionality to update obs to disk

3fc534b

add plotting support for non memory backed h5sc files

d20b5ac

Merge branch 'main' into add_tutorial_roi_regions

fd66e0f

rename function

14b0bc3

parametrize function

ec810f8

add print statement

c67cade

Merge pull request #104 from MannLabs/Add_tissue_region_masking

bee60c7

Add function to mask tissue regions

simplify code structure and remove duplicate function

60b1f52

[FEATURE] add functions to subset h5sc objects

f6d636a

ruff linting and fix pre-commit issues

7efb1ff

add general synthetic test objects that closely mimic real objects

ba50312

[TEST] improve h5sc plotting tests

471a8e6

[TESTS] add tests for h5sc operations

04ca7e8

doesn't yet cover all functions

Merge branch 'main' into add_tutorial_roi_regions

544e4c5

sophiamaedler and others added 11 commits January 4, 2026 11:40

Merge branch 'main' into add_tutorial_roi_regions

edd376c

[pre-commit.ci] auto fixes from pre-commit.com hooks

9823f94

for more information, see https://pre-commit.ci

Merge branch 'main' into add_tutorial_roi_regions

37bef6d

[FIX] incorrect warning condition

d3f488e

[FIX] docstrings and import statements

e746ca5

[FEATURE] first working version of the mask_region function

c3ab5b5

[TEST] add tests for _subset module

6c35a42

[FIX] update requirements to support new mask region function

f95f48f

[FIX] add missing requirement

15cc8ae

[FIX] also support numpy obsm values not just hdf5 backed

3b85f15

Merge branch 'main' into add_tutorial_roi_regions

3fa889b

Copilot AI review requested due to automatic review settings February 5, 2026 10:38

[pre-commit.ci] auto fixes from pre-commit.com hooks

8e1b423

for more information, see https://pre-commit.ci

Copilot AI reviewed Feb 5, 2026

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Add tutorial roi regions#330

Add tutorial roi regions#330
sophiamaedler wants to merge 29 commits intomainfrom
add_tutorial_roi_regions

sophiamaedler commented Nov 6, 2025 •

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	if not isinstance(outpath, (str \| Path)):
	if not isinstance(outpath, (str, Path)):

		# Load a fresh AnnData
		adata = read_h5sc(self.extraction_f.output_path or self.extraction_f.extraction_file)

-        # Load a fresh AnnData
-        adata = read_h5sc(self.extraction_f.output_path or self.extraction_f.extraction_file)
+        # Ensure extraction configuration is available before accessing its attributes
+        extraction_f = getattr(self, "extraction_f", None)
+        if extraction_f is None:
+            raise ValueError(
+                "Extraction configuration 'extraction_f' is not set. "
+                "Run the extraction step before accessing 'h5sc'."
+            )
+        # Load a fresh AnnData
+        adata = read_h5sc(extraction_f.output_path or extraction_f.extraction_file)

	if any(channel_names_old != channel_names):
	if channel_names_old != channel_names:

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sophiamaedler commented Nov 6, 2025 •

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