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Write points fix #15

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will-moore wants to merge 2 commits into from
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Write points fix #15

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246da48
Unify table writing for points, regions etc
will-moore Mar 14, 2023
0405305
Remove print
will-moore Mar 14, 2023
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33 changes: 21 additions & 12 deletions src/ngff_tables_prototype/writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,7 @@ def write_table_points(
table_group_name: str = "points_table",
group_type: str = "ngff:points_table",
):
write_elem(group, table_group_name, adata)
table_group = group[table_group_name]
table_group.attrs["type"] = group_type
write_table_data(group, adata, table_group_name, group_type)


def write_table_polygons(
Expand All @@ -28,9 +26,7 @@ def write_table_polygons(
table_group_name: str = "polygons_table",
group_type: str = "ngff:polygons_table",
):
write_elem(group, table_group_name, adata)
table_group = group[table_group_name]
table_group.attrs["type"] = group_type
write_table_data(group, adata, table_group_name, group_type)


def write_table_circles(
Expand All @@ -39,9 +35,7 @@ def write_table_circles(
table_group_name: str = "circles_table",
group_type: str = "ngff:circles_table",
):
write_elem(group, table_group_name, adata)
table_group = group[table_group_name]
table_group.attrs["@type"] = group_type
write_table_data(group, adata, table_group_name, group_type)


def write_table_regions(
Expand All @@ -52,6 +46,18 @@ def write_table_regions(
region: Union[str, List[str]] = "features",
region_key: Optional[str] = None,
instance_key: Optional[str] = None,
):
write_table_data(group, adata, table_group_name, group_type, region, region_key, instance_key)


def write_table_data(
group: zarr.Group,
adata: AnnData,
table_group_name: str,
group_type: str = "ngff:regions_table",
region: Optional[Union[str, List[str]]] = None,
region_key: Optional[str] = None,
instance_key: Optional[str] = None,
):
write_elem(group, table_group_name, adata)
# add table_group_name to "tables" list
Expand All @@ -60,9 +66,12 @@ def write_table_regions(
group.attrs["tables"] = table_attrs
table_group = group[table_group_name]
table_group.attrs["type"] = group_type
table_group.attrs["region"] = region
table_group.attrs["region_key"] = region_key
table_group.attrs["instance_key"] = instance_key
if region_key is not None:
table_group.attrs["region"] = region
if region_key is not None:
table_group.attrs["region_key"] = region_key
if instance_key is not None:
table_group.attrs["instance_key"] = instance_key

# Simple, local "consolidate_metadata" to list child groups
def index_group(grp_name):
Expand Down