Make seed health checks optional in synthesizers.

riid/data/synthetic/passby.py

@@ -225,7 +225,8 @@ def _generate_single_passby(self, fwhm: float, snr: float, dwell_time: float,
 
         return fg_ss, gross_ss
 
-    def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet, verbose: bool = True) \
+    def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet,
+                 skip_health_check: bool = False, verbose: bool = True) \
             -> List[Tuple[SampleSet, SampleSet, SampleSet]]:
         """Generate a list of `SampleSet`s where each contains a pass-by as a sequence of spectra.
 
@@ -234,6 +235,7 @@ def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet, verbose: bool
                 source component(s) of spectra
             bg_seeds_ss: spectra normalized by total counts to be used as the
                 background components of gross spectra
+            skip_health_check: whether to skip seed health checks
             verbose: whether to display output from synthesis
 
         Returns:
@@ -245,8 +247,10 @@ def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet, verbose: bool
         """
         if not fg_seeds_ss or not bg_seeds_ss:
             raise ValueError("At least one foreground and background seed must be provided.")
-        fg_seeds_ss.check_seed_health()
-        bg_seeds_ss.check_seed_health()
+
+        if not skip_health_check:
+            fg_seeds_ss.check_seed_health()
+            bg_seeds_ss.check_seed_health()
 
         self._reset_progress()
         if verbose:

riid/data/synthetic/seed.py

@@ -166,8 +166,9 @@ def __init__(self, seeds_ss: SampleSet, mixture_size: int = 2, dirichlet_alpha:
 
         self._check_seeds()
 
-    def _check_seeds(self):
-        self.seeds_ss.check_seed_health()
+    def _check_seeds(self, skip_health_check: bool = False):
+        if not skip_health_check:
+            self.seeds_ss.check_seed_health()
         n_sources_per_row = np.count_nonzero(
             self.seeds_ss.get_source_contributions(),
             axis=1
@@ -187,7 +188,8 @@ def _check_seeds(self):
                     "All seeds must have the same energy calibration."
                 ))
 
-    def __call__(self, n_samples: int, max_batch_size: int = 100) -> Iterator[SampleSet]:
+    def __call__(self, n_samples: int, max_batch_size: int = 100,
+                 skip_health_check: bool = False) -> Iterator[SampleSet]:
         """Yields batches of seeds one at a time until a specified number of samples has
         been reached.
 
@@ -204,12 +206,13 @@ def __call__(self, n_samples: int, max_batch_size: int = 100) -> Iterator[Sample
 
         Args:
             n_samples: total number of mixture seeds to produce across all batches
-            max_batch_size: maxmimum size of a batch per yield
+            max_batch_size: maximum size of a batch per yield
+            skip_health_check: whether to skip the seed health check
 
         Returns:
             Generator of `SampleSet`s
         """
-        self._check_seeds()
+        self._check_seeds(skip_health_check)
 
         isotope_to_seeds = self.seeds_ss.sources_columns_to_dict(target_level="Isotope")
         isotopes = list(isotope_to_seeds.keys())
@@ -298,11 +301,17 @@ def __call__(self, n_samples: int, max_batch_size: int = 100) -> Iterator[Sample
 
             yield batch_ss
 
-    def generate(self, n_samples: int, max_batch_size: int = 100) -> SampleSet:
+    def generate(self, n_samples: int, max_batch_size: int = 100,
+                 skip_health_check: bool = False) -> SampleSet:
         """Computes random mixtures of seeds at the isotope level.
         """
         batches = []
-        for batch_ss in self(n_samples, max_batch_size=max_batch_size):
+        batch_iterable = self(
+            n_samples,
+            max_batch_size=max_batch_size,
+            skip_health_check=skip_health_check
+        )
+        for batch_ss in batch_iterable:
             batches.append(batch_ss)
         mixtures_ss = SampleSet()
         mixtures_ss.spectra_type = self.seeds_ss.spectra_type

riid/data/synthetic/static.py

@@ -220,6 +220,7 @@ def _get_synthetic_samples(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet,
         return fg_ss, gross_ss
 
     def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet,
+                 skip_health_check: bool = False,
                  verbose: bool = True) -> Tuple[SampleSet, SampleSet]:
         """Generate a `SampleSet` of gamma spectra from the provided config.
 
@@ -240,6 +241,7 @@ def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet,
                 `bg_seeds_ss`, which represent mixtures of K-U-T, get added on top.
                 Note: this spectrum is not considered part of the `bg_cps` parameter,
                 but is instead added on top of it.
+            skip_health_check: whether to skip seed health checks
             verbose: whether to show detailed output
 
         Returns:
@@ -251,8 +253,9 @@ def generate(self, fg_seeds_ss: SampleSet, bg_seeds_ss: SampleSet,
         """
         if not fg_seeds_ss or not bg_seeds_ss:
             raise ValueError("At least one foreground and background seed must be provided.")
-        fg_seeds_ss.check_seed_health()
-        bg_seeds_ss.check_seed_health()
+        if not skip_health_check:
+            fg_seeds_ss.check_seed_health()
+            bg_seeds_ss.check_seed_health()
 
         self._reset_progress()
         if verbose: