Add method runtime parameters to logging

starfish/core/pipeline/algorithmbase.py

@@ -25,19 +25,19 @@ def helper(*args, **kwargs):
                 method_class_str = str(args[0].__class__)
                 if 'ApplyTransform' in method_class_str or 'Filter' in method_class_str:
                     # Update the log on the resulting ImageStack
-                    result.log.update_log(args[0])
+                    result.log.update_log(args[0], kwargs)
                 if 'FindSpots' in method_class_str:
                     # Update the log on the resulting SpotFindingResults
-                    result.log.update_log(args[0])
+                    result.log.update_log(args[0], kwargs)
                 if 'DecodeSpots' in method_class_str:
                     # update log then transfer to DecodedIntensityTable
                     spot_results = kwargs['spots']
-                    spot_results.log.update_log(args[0])
+                    spot_results.log.update_log(args[0], kwargs)
                     result.attrs[STARFISH_EXTRAS_KEY] = spot_results.log.encode()
                 if 'DetectPixels' in method_class_str:
                     stack = args[1]
                     # update log with spot detection instance args[0]
-                    stack.log.update_log(args[0])
+                    stack.log.update_log(args[0], kwargs)
                     # get resulting intensity table and set log
                     it = result[0]
                     it.attrs[STARFISH_EXTRAS_KEY] = stack.log.encode()

starfish/core/util/logging.py

@@ -18,20 +18,23 @@ def __init__(self):
         """
         self._log: List[dict] = list()
 
-    def update_log(self, class_instance) -> None:
+    def update_log(self, class_instance, method_runtime_parameters=None) -> None:
         """
         Adds a new entry to the log list.
 
         Parameters
         ----------
         class_instance: The instance of a class being applied to the imagestack
+
+        method_runtime_parameters: Any runtime parameters passed to the method
         """
         entry = {"method": class_instance.__class__.__name__,
+                 "method_runtime_parameters": method_runtime_parameters,
                  "arguments": class_instance.__dict__,
                  "os": get_os_info(),
                  "dependencies": get_core_dependency_info(),
                  "release tag": get_release_tag(),
-                 "starfish version": get_dependency_version('starfish')
+                 "starfish version": get_dependency_version('starfish'),
                  }
         self._log.append(entry)
 

starfish/test/full_pipelines/api/test_iss_api.py

@@ -123,6 +123,7 @@ def test_iss_pipeline_cropped_data(tmpdir):
 
     assert pipeline_log[0]['method'] == 'WhiteTophat'
     assert pipeline_log[1]['method'] == 'Warp'
+    assert 'transforms_list' in pipeline_log[1]['method_runtime_parameters']
     assert pipeline_log[2]['method'] == 'BlobDetector'
     assert pipeline_log[3]['method'] == 'PerRoundMaxChannel'