Fix counts provided for specimens without cells in the selected cell …

…list (#252)

* no cells selected in specimen return None

* adjust none condition

* forgot to add another None type to PhenotypeCount

* update a type hint

spatialprofilingtoolbox/db/exchange_data_formats/metrics.py

@@ -60,8 +60,8 @@ class PhenotypeCount(BaseModel):
     belonging to some specific class.
     """
     specimen: str
-    count: int
-    percentage: float
+    count: int | None
+    percentage: float | None
 
 
 class PhenotypeCounts(BaseModel):

spatialprofilingtoolbox/ondemand/providers/counts_provider.py

@@ -34,9 +34,9 @@ def count_structures_of_partial_signed_signature(
         negatives_signature: int,
         measurement_study: str,
         cells_selected: tuple[int, ...] | None = None,
-    ) -> dict[str, list[int]]:
+    ) -> dict[str, tuple[int, int] | tuple[None, None]]:
         """Count the number of structures per specimen that match this signature."""
-        counts: dict[str, list[int]] = {}
+        counts: dict[str, tuple[int, int] | tuple[None, None]] = {}
         selection = Index(list(cells_selected)) if cells_selected else None
         for specimen, data_array in self.data_arrays[measurement_study].items():
             count = 0
@@ -48,10 +48,10 @@ def count_structures_of_partial_signed_signature(
                 data_array.loc[data_array.index.intersection(selection), 'integer'],
             )
             if len(integers) == 0:
-                message = 'Cell subselection %s resulted in no cells for specimen %s'
-                raise ValueError(message, cells_selected, specimen)
+                counts[specimen] = (None, None)
+                continue
             count = self.get_count(integers, positives_signature, negatives_signature)
-            counts[specimen] = [count, len(integers)]
+            counts[specimen] = (count, len(integers))
         return counts
 
     def get_count(self, integers: list[int], positives_mask: int, negatives_mask: int) -> int:

spatialprofilingtoolbox/ondemand/request_handler.py

@@ -99,7 +99,7 @@ def _get_counts(
         positives_signature: int,
         negatives_signature: int,
         cells_selected: set[int] | None = None,
-    ) -> dict[str, list[int]]:
+    ) -> dict[str, tuple[int, int] | tuple[None, None]]:
         assert self.server.providers.counts is not None
         measurement_study = self._get_measurement_study(study)
         return self.server.providers.counts.count_structures_of_partial_signed_signature(

spatialprofilingtoolbox/ondemand/service_client.py

@@ -59,6 +59,7 @@ def get_counts_by_specimen(
                     specimen=specimen,
                     count=count,
                     percentage=self._fancy_round(count / count_all_in_specimen)
+                    if ((count is not None) and (count_all_in_specimen not in {0, None})) else None,
                 )
                 for specimen, (count, count_all_in_specimen) in response.items()
             ],