def build_spot_traces_exact_match(spot_results: SpotFindingResults,
**kwargs) -> IntensityTable:
"""
Combines spots found in matching x/y positions across rounds and channels of
an ImageStack into traces represented as an IntensityTable.
Parameters
-----------
spot_results: SpotFindingResults
Spots found across rounds/channels of an ImageStack
"""
# create IntensityTable with same x/y/z info accross all r/ch
spot_attributes = list(spot_results.values())[0].spot_attrs
intensity_table = IntensityTable.zeros(
spot_attributes=spot_attributes,
round_labels=spot_results.round_labels,
ch_labels=spot_results.ch_labels,
)
for r, c in spot_results.keys():
value = spot_results[{
Axes.ROUND: r,
Axes.CH: c
}].spot_attrs.data[Features.INTENSITY]
# if no exact match set value to 0
value = 0 if value.empty else value
intensity_table.loc[dict(c=c, r=r)] = value
return intensity_table
def build_traces_sequential(spot_results: SpotFindingResults,
**kwargs) -> IntensityTable:
"""
Build spot traces without merging across channels and imaging rounds. Used for sequential
methods like smFIsh.
Parameters
----------
spot_results: SpotFindingResults
Spots found across rounds/channels of an ImageStack
Returns
-------
IntensityTable :
concatenated input SpotAttributes, converted to an IntensityTable object
"""
all_spots = pd.concat([sa.data for sa in spot_results.values()], sort=True)
intensity_table = IntensityTable.zeros(
spot_attributes=SpotAttributes(all_spots),
ch_labels=spot_results.ch_labels,
round_labels=spot_results.round_labels,
)
i = 0
for (r, c), attrs in spot_results.items():
for _, row in attrs.data.iterrows():
selector = dict(features=i, c=c, r=r)
intensity_table.loc[selector] = row[Features.INTENSITY]
i += 1
return intensity_table
