Tiny changes to address gaussian noise parameters in input files

compSPI · Dec 12, 2021 · 6d03b19 · 6d03b19
1 parent cd7a691
commit 6d03b19
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 2 deletions.
diff --git a/ioSPI/cryoemio.py b/ioSPI/cryoemio.py
@@ -131,6 +131,8 @@ def fill_parameters_dictionary(
 
     *** miscellaneous ***
     - seed [OPTIONAL]              : seed for the run. If not present, random.
+    - signal_to_noise [OPTIONAL]   : signal-to-noise ratio for gaussian white noise.
+    - signal_to_noise_db [OPTIONAL] : signal-to-noise ratio in decibels.
     """
     parameters = None
     with open(input_params_file, "r") as f:
@@ -143,6 +145,17 @@ def fill_parameters_dictionary(
     except KeyError:
         random.seed()
         dic["simulation"]["seed"] = random.randint(0, int(1e10))
+    dic["other"] = {}
+    try:
+        dic["other"]["signal_to_noise"] = parameters["miscellaneous"]["signal_to_noise"]
+    except KeyError:
+        pass
+    try:
+        dic["other"]["signal_to_noise_db"] = parameters["miscellaneous"][
+            "signal_to_noise_db"
+        ]
+    except KeyError:
+        pass
     dic["simulation"]["log_file"] = log_file
     dic["sample"] = {}
     dic["sample"]["diameter"] = parameters["specimen_grid_params"]["hole_diameter_nm"]

diff --git a/tests/test_cryoemio.py b/tests/test_cryoemio.py
@@ -64,9 +64,11 @@ def test_fill_parameters_dictionary_max():
     noise = "no"
     detector_q_efficiency = 0.1
     mtf_params = [0.1, 0.0, 0.7, 0, 0]
-    noise_override = 0.1
+    noise_override = "yes"
     log_file = "itslog.log"
     seed = 210
+    snr = 0.6
+    snr_db = 10
     key = particle_mrcout.split(".mrc")[0]
 
     try:
@@ -109,7 +111,11 @@ def test_fill_parameters_dictionary_max():
                     "detector_Q_efficiency": detector_q_efficiency,
                     "MTF_params": mtf_params,
                 },
-                "miscellaneous": {"seed": seed},
+                "miscellaneous": {
+                    "seed": seed,
+                    "signal_to_noise": snr,
+                    "signal_to_noise_db": snr_db,
+                },
             }
             contents = yaml.dump(data)
             f.write(contents)
@@ -167,6 +173,9 @@ def test_fill_parameters_dictionary_max():
         assert out_dict["detector"]["mtf_alpha"] == mtf_params[3]
         assert out_dict["detector"]["mtf_beta"] == mtf_params[4]
         assert out_dict["detector"]["image_file_out"] == mrc_file
+
+        assert out_dict["other"]["signal_to_noise"] == snr
+        assert out_dict["other"]["signal_to_noise_db"] == snr_db
     finally:
         os.unlink(tmp_yml.name)