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feat(io): optional z-coordinate passthrough (include_z, default False) #57

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feat(io): optional z-coordinate passthrough (include_z, default False) #57

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2 changes: 2 additions & 0 deletions src/segger/io/fields.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ class XeniumTranscriptFields:
filename: str = 'transcripts.parquet'
x: str = 'x_location'
y: str = 'y_location'
z: str = 'z_location'
feature: str = 'feature_name'
cell_id: str = 'cell_id'
null_cell_id: str = 'UNASSIGNED'
Expand Down Expand Up @@ -107,6 +108,7 @@ class StandardTranscriptFields:
row_index: str = 'row_index'
x: str = 'x'
y: str = 'y'
z: str = 'z'
feature: str = 'feature_name'
cell_id: str = 'cell_id'
compartment: str = 'cell_compartment'
Expand Down
21 changes: 15 additions & 6 deletions src/segger/io/preprocessor.py
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Expand Up @@ -63,7 +63,7 @@ class ISTPreprocessor(ABC):
transcript and boundary GeoDataFrames for the given platform.
"""

def __init__(self, data_dir: Path):
def __init__(self, data_dir: Path, include_z: bool = False):
"""
Parameters
----------
Expand All @@ -73,6 +73,7 @@ def __init__(self, data_dir: Path):
data_dir = Path(data_dir)
type(self)._validate_directory(data_dir)
self.data_dir = data_dir
self.include_z = include_z

@staticmethod
@abstractmethod
Expand Down Expand Up @@ -287,11 +288,10 @@ def transcripts(self) -> pl.DataFrame:
.alias(std.cell_id)
)
# Map to standard field names
.rename({raw.x: std.x, raw.y: std.y, raw.feature: std.feature})
.rename(rename_map)

# Subset to necessary fields
.select([std.row_index, std.x, std.y, std.feature, std.cell_id,
std.compartment])
.select(select_cols)

# Add numeric index
.with_row_index()
Expand Down Expand Up @@ -405,6 +405,14 @@ def transcripts(self) -> pl.DataFrame:
raw = self.tx_fields
std = StandardTranscriptFields()

rename_map = {raw.x: std.x, raw.y: std.y, raw.feature: std.feature}
select_cols = [
std.row_index, std.x, std.y, std.feature, std.cell_id, std.compartment,
]
if self.include_z:
rename_map[raw.z] = std.z
select_cols.append(std.z)

return (
# Read in lazily
pl.scan_parquet(
Expand Down Expand Up @@ -564,7 +572,8 @@ def _infer_platform(data_dir: Path) -> str:

def get_preprocessor(
data_dir: Path,
platform: str | None = None
platform: str | None = None,
include_z: bool = False,
) -> ISTPreprocessor:
data_dir = Path(data_dir)
if platform is None:
Expand All @@ -575,4 +584,4 @@ def get_preprocessor(
f"Available: {list(PREPROCESSORS)}"
)
cls = PREPROCESSORS[platform.lower()]
return cls(data_dir)
return cls(data_dir, include_z=include_z)