Add expanded config support to SeedSynthesizer.

Co-authored-by: Alan Van Omen <[email protected]>

examples/data/synthesis/synthesize_seeds_advanced.py

@@ -0,0 +1,81 @@
+# Copyright 2021 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+# Under the terms of Contract DE-NA0003525 with NTESS,
+# the U.S. Government retains certain rights in this software.
+"""This example demonstrates how to generate synthetic seeds from GADRAS using PyRIID's
+configuration expansion features."""
+import yaml
+
+from riid.data.synthetic.seed import SeedSynthesizer
+from riid.gadras.api import get_expanded_config, validate_inject_config
+
+seed_synth_config = """
+---
+gamma_detector:
+  name: Generic\\NaI\\2x4x16
+  parameters:
+    distance_cm:
+      - 10
+      - 100
+      - 1000
+    height_cm: 100
+    dead_time_per_pulse: 5
+    latitude_deg: 35.0
+    longitude_deg: 253.4
+    elevation_m: 1620
+sources:
+  - isotope: Cs137
+    configurations:
+      - Cs137,100uCi
+      - name: Cs137
+        activity:
+          - 1
+          - 0.5
+        activity_units: Ci
+        shielding_atomic_number:
+          min: 10
+          max: 40.0
+          dist: uniform
+          num_samples: 5
+        shielding_aerial_density:
+          mean: 120
+          std: 2
+          num_samples: 5
+  - isotope: Cosmic
+    configurations:
+      - Cosmic
+  - isotope: K40
+    configurations:
+      - PotassiumInSoil
+  - isotope: Ra226
+    configurations:
+      - UraniumInSoil
+  - isotope: Th232
+    configurations:
+      - ThoriumInSoil
+...
+"""
+seed_synth_config = yaml.safe_load(seed_synth_config)
+validate_inject_config(seed_synth_config)
+from pprint import pprint
+pprint(len(get_expanded_config(seed_synth_config)["sources"][0]["configurations"]))
+
+try:
+    seeds_ss = SeedSynthesizer().generate(
+        seed_synth_config,
+        verbose=True
+    )
+    print(seeds_ss)
+
+    # At this point, you could save out the seeds via:
+    seeds_ss.to_hdf("seeds.h5")
+
+    # or start separating your backgrounds from foreground for use with the StaticSynthesizer
+    fg_seeds_ss, bg_seeds_ss = seeds_ss.split_fg_and_bg()
+
+    print(fg_seeds_ss)
+    print(bg_seeds_ss)
+
+    fg_seeds_ss.to_hdf("./fg_seeds.h5")
+    bg_seeds_ss.to_hdf("./bg_seeds.h5")
+except FileNotFoundError:
+    pass  # Happens when not on Windows

riid/data/synthetic/seed.py

@@ -15,7 +15,7 @@
 from riid.data.sampleset import SampleSet, _get_utc_timestamp, read_pcf
 from riid.gadras.api import (DETECTOR_PARAMS, GADRAS_ASSEMBLY_PATH,
                              INJECT_PARAMS, SourceInjector, get_gadras_api,
-                             validate_inject_config)
+                             get_inject_setups, validate_inject_config)
 
 
 class SeedSynthesizer():
@@ -65,7 +65,7 @@ def _set_detector_parameters(self, gadras_api, new_parameters: dict, verbose=Fal
 
     def generate(self, config: Union[str, dict],
                  normalize_spectra: bool = True, normalize_sources: bool = True,
-                 dry_run=False, verbose: bool = False) -> SampleSet:
+                 verbose: bool = False) -> SampleSet:
         """Produce a `SampleSet` containing foreground and/or background seeds using GADRAS based
         on the given inject configuration.
 
@@ -75,8 +75,6 @@ def generate(self, config: Union[str, dict],
                 file which deserialized as a dictionary
             normalize_spectra: whether to divide each row of `SampleSet.spectra` by each row's sum
             normalize_sources: whether to divide each row of `SampleSet.sources` by each row's sum
-            dry_run: when False, actually perform inject(s), otherwise simply report info about
-                what would hypothetically happen
             verbose: whether to show detailed output
 
         Returns:
@@ -95,30 +93,25 @@ def generate(self, config: Union[str, dict],
 
         validate_inject_config(config)
 
+        setups = get_inject_setups(config)
         with self._cwd(GADRAS_ASSEMBLY_PATH):
             gadras_api = get_gadras_api()
             detector_name = config["gamma_detector"]["name"]
-            new_detector_parameters = config["gamma_detector"]["parameters"]
             gadras_api.detectorSetCurrent(detector_name)
             original_detector_parameters = self._get_detector_parameters(gadras_api)
-            now = _get_utc_timestamp().replace(":", "_")  # replace() prevents error on Windows
-
-            rel_output_path = f"{now}_sources.pcf"
-            source_list = []
-            detector_setups = [new_detector_parameters]  # TODO: generate all detector_setups
             source_injector = SourceInjector(gadras_api)
-            try:
-                for d in detector_setups:
-                    self._set_detector_parameters(gadras_api, d, verbose, dry_run)
-
-                    if dry_run:
-                        continue
-
+            if verbose:
+                print(f"Obtaining sources for '{detector_name}'")
+
+            for s in setups:
+                new_detector_parameters = s["gamma_detector"]["parameters"]
+                now = _get_utc_timestamp().replace(":", "_")  # replace() prevents error on Windows
+                rel_output_path = f"{now}_sources.pcf"
+                source_list = []
+                try:
+                    self._set_detector_parameters(gadras_api, new_detector_parameters, verbose)
                     # TODO: propagate dry_run to injectors
-
                     # Source injects
-                    if verbose:
-                        print(f"Obtaining sources for '{detector_name}'")
                     pcf_abs_path = source_injector.generate(
                         config,
                         rel_output_path,
@@ -130,22 +123,13 @@ def generate(self, config: Union[str, dict],
                     if normalize_spectra:
                         seeds_ss.normalize()
                     source_list.append(seeds_ss)
-
-                    if verbose:
-                        print()
-
-                if dry_run:
-                    return None
-
-            except Exception as e:
-                # Try to restore .dat file to original state even when an error occurs
-                if not dry_run:
+                except Exception as e:
+                    # Try to restore .dat file to original state even when an error occurs
                     self._set_detector_parameters(gadras_api, original_detector_parameters)
-                raise e
+                    raise e
 
             # Restore .dat file to original state
-            if not dry_run:
-                self._set_detector_parameters(gadras_api, original_detector_parameters)
+            self._set_detector_parameters(gadras_api, original_detector_parameters)
 
         ss = SampleSet()
         ss.concat(source_list)

riid/gadras/api.py

@@ -535,15 +535,19 @@ def get_expanded_config(config: dict) -> dict:
     return expanded_config
 
 
-def get_detector_setups(expanded_config: dict):
-    """
-    Permutate the lists of values in the expanded config to
+def get_detector_setups(expanded_config: dict) -> list:
+    """Permutate the lists of values in the expanded config to
     generate a list of detector setups.
+
+    Args:
+        expanded_config: a dictionary representing an expanded seed synthesis configuration
+
+    Returns:
+        A list of detector setups
     """
     detector_params = expanded_config["gamma_detector"]["parameters"]
     list_of_parameters_values = [x for x in detector_params.values()]
     parameter_permutations = list(itertools.product(*list_of_parameters_values))
-
     detector_setups = []
     for perm in parameter_permutations:
         setup = copy.deepcopy(expanded_config["gamma_detector"])
@@ -554,13 +558,17 @@ def get_detector_setups(expanded_config: dict):
     return detector_setups
 
 
-def get_inject_setups(config: dict):
-    """
-    Creates a list of dictionaries containing the individual detector_setups with
-    expanded sources.
+def get_inject_setups(config: dict) -> list:
+    """Get a list of fully expanded synthesis configurations from an initial,
+    collapsed configuration.
+
+    Args:
+        config: a dictionary representing a collapsed seed synthesis configuration
+
+    Returns:
+        A list of expanded configurations
     """
     expanded_config = get_expanded_config(config)
-
     detector_setups = get_detector_setups(expanded_config)
     inject_setups = []
     for detector_setup in detector_setups: