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Merged
keviny2 merged 12 commits into from
Feb 26, 2025
Merged

combine column ops #23

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c468714
Write function stubs
keviny2 Feb 17, 2025
745cd06
Begin implementing combine_columns
keviny2 Feb 18, 2025
54030ec
Make deepcopy of coldata
keviny2 Feb 21, 2025
108ba1f
Add test for duplicate sample ids for combine ops
keviny2 Feb 21, 2025
76b0d65
Add row_names and column_names to test spe
keviny2 Feb 24, 2025
e7566ca
WIP: Add test for checking that img_data combined correctly
keviny2 Feb 25, 2025
0c650db
All combine columns tests pass
keviny2 Feb 25, 2025
b463d71
Lint
keviny2 Feb 25, 2025
3d54703
Handle relaxed combine columns
keviny2 Feb 26, 2025
4a625ad
Test relaxed combine columns
keviny2 Feb 26, 2025
017feb7
Make type hints compatable with python<=3.10
keviny2 Feb 26, 2025
9520b7f
Update CHANGELOG
keviny2 Feb 26, 2025
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Changelog

## Version 0.0.6
- Added `combine_columns` function
- Implemented `__eq__` override for `SpatialImage` subclasses

## Version 0.0.5

- Implementing a placeholder `SpatialFeatureExperiment` class. This version only implements the data structure to hold various geometries but none of the methods except for slicing.
Expand Down
55 changes: 42 additions & 13 deletions src/spatialexperiment/ProxySFE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,11 @@
from summarizedexperiment._frameutils import _sanitize_frame
from summarizedexperiment.RangedSummarizedExperiment import GRangesOrGRangesList

from .SpatialExperiment import SpatialExperiment, _validate_column_data, _validate_sample_ids
from .SpatialExperiment import (
SpatialExperiment,
_validate_column_data,
_validate_sample_ids,
)

__author__ = "jkanche"
__copyright__ = "jkanche"
Expand Down Expand Up @@ -44,7 +48,10 @@ def _validate_geometries(geometries: Dict[str, gpd.GeoDataFrame], prop_name: str

for i, geom in enumerate(geometries.values()):
if not isinstance(geom, gpd.GeoDataFrame):
raise TypeError(f"Item {i} in {prop_name} is {type(geom).__name__} " f"rather than `GeoDataFrame`.\n")
raise TypeError(
f"Item {i} in {prop_name} is {type(geom).__name__} "
f"rather than `GeoDataFrame`.\n"
)


def _validate_annotgeometries(geometries, column_data):
Expand All @@ -58,13 +65,16 @@ def _validate_annotgeometries(geometries, column_data):

for i, geom in enumerate(geometries.values()):
if "sample_id" not in geom.columns:
raise ValueError(f"Item {i} of 'annot_geometries' does not have column 'sample_id'.\n")
raise ValueError(
f"Item {i} of 'annot_geometries' does not have column 'sample_id'.\n"
)
else:
samples_seen = geom["sample_id"].unique()
missing = [s for s in samples_seen if s not in sample_ids]
if len(missing) > 0:
raise ValueError(
f"Samples {', '.join(missing)} in item {i} of " f"annot_geometries are absent from 'column_data'.\n"
f"Samples {', '.join(missing)} in item {i} of "
f"annot_geometries are absent from 'column_data'.\n"
)


Expand All @@ -75,7 +85,9 @@ def _validate_graph_sample_id(spatial_graphs, column_data):

missing = graph_sample_ids - col_sample_ids
if missing:
raise ValueError(f"Samples {', '.join(missing)} are in the graphs but not 'column_data'.\n")
raise ValueError(
f"Samples {', '.join(missing)} are in the graphs but not 'column_data'.\n"
)


def _validate_graph_structure(spatial_graphs):
Expand All @@ -89,7 +101,9 @@ def _validate_graph_structure(spatial_graphs):
"and whose rows are margins (rows, columns, annotation).\n"
)
elif not set(spatial_graphs.get_row_names()) == {"row", "col", "annot"}:
raise ValueError("Row names of 'spatial_graphs' must be 'row', 'col', and 'annot'.\n")
raise ValueError(
"Row names of 'spatial_graphs' must be 'row', 'col', and 'annot'.\n"
)


class ProxySpatialFeatureExperiment(SpatialExperiment):
Expand Down Expand Up @@ -404,7 +418,9 @@ def __repr__(self) -> str:

output += ", col_geometries=" + ut.print_truncated_dict(self._col_geometries)
output += ", row_geometries=" + ut.print_truncated_dict(self._row_geometries)
output += ", annot_geometries=" + ut.print_truncated_dict(self._annot_geometries)
output += ", annot_geometries=" + ut.print_truncated_dict(
self._annot_geometries
)

output += ", spatial_graphs=" + self._spatial_graphs.__repr__()
output += ")"
Expand Down Expand Up @@ -448,7 +464,9 @@ def get_unit(self) -> str:
"""Get the coordinate unit."""
return self._unit

def set_unit(self, unit: str, in_place: bool = False) -> "ProxySpatialFeatureExperiment":
def set_unit(
self, unit: str, in_place: bool = False
) -> "ProxySpatialFeatureExperiment":
"""Set the coordinate unit.

Args:
Expand Down Expand Up @@ -631,7 +649,9 @@ def set_spatial_graphs(
Returns:
A modified ``ProxySpatialFeatureExperiment`` object, either as a copy of the original or as a reference to the (in-place-modified) original.
"""
_graphs = _sanitize_spatial_graphs(graphs, list(set(self.get_column_data().get_column("sample_id"))))
_graphs = _sanitize_spatial_graphs(
graphs, list(set(self.get_column_data().get_column("sample_id")))
)
_validate_graph_structure(_graphs)
_validate_graph_sample_id(_graphs, self.get_column_data())

Expand All @@ -658,7 +678,9 @@ def spatial_graphs(self, graphs: Optional[BiocFrame]):
################################

def get_slice(
self, rows: Optional[Union[str, int, bool, List]] = None, columns: Optional[Union[str, int, bool, List]] = None
self,
rows: Optional[Union[str, int, bool, List]] = None,
columns: Optional[Union[str, int, bool, List]] = None,
) -> "ProxySpatialFeatureExperiment":
"""Get a slice of the experiment.

Expand All @@ -675,7 +697,9 @@ def get_slice(
sfe = super().get_slice(rows=rows, columns=columns)

slicer = self._generic_slice(rows=rows, columns=columns)
do_slice_cols = not (isinstance(slicer.col_indices, slice) and slicer.col_indices == slice(None))
do_slice_cols = not (
isinstance(slicer.col_indices, slice) and slicer.col_indices == slice(None)
)

# Update geometries and graphs
if do_slice_cols:
Expand All @@ -698,7 +722,9 @@ def get_slice(
new_graphs = None
if self.spatial_graphs is not None:
# Keep only columns for remaining samples
cols_to_keep = [c for c in self.spatial_graphs.columns if c in column_sample_ids]
cols_to_keep = [
c for c in self.spatial_graphs.columns if c in column_sample_ids
]
if cols_to_keep:
new_graphs = self.spatial_graphs[cols_to_keep]

Expand Down Expand Up @@ -743,7 +769,10 @@ def get_slice(
################################

def set_column_data(
self, cols: Optional[BiocFrame], replace_column_names: bool = False, in_place: bool = False
self,
cols: Optional[BiocFrame],
replace_column_names: bool = False,
in_place: bool = False,
) -> "ProxySpatialFeatureExperiment":
"""Override: Set sample data.

Expand Down
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