Debugged info addition when processing locs

picasso_workflow/analyse.py

@@ -56,11 +56,14 @@ def module_wrapper(self, i, parameters):
             if parameters.get("save_locs") is True or self.analysis_config.get(
                 "always_save"
             ):
-                if hasattr(self, "locs"):
+                if hasattr(self, "locs") and self.locs is not None:
                     self._save_locs(
                         os.path.join(results["folder"], "locs.hdf5")
                     )
-                if hasattr(self, "channel_locs"):
+                if (
+                    hasattr(self, "channel_locs")
+                    and self.channel_locs is not None
+                ):
                     self._save_datasets_agg(results["folder"])
         results["end time"] = datetime.now().strftime("%y-%m-%d %H:%M:%S")
         td = datetime.strptime(
@@ -524,6 +527,16 @@ def identify(self, i, parameters, results):
                     results["folder"], pars["filename"]
                 )
             results["ids_vs_frame"] = self._plot_ids_vs_frame(**pars)
+
+        # add info
+        new_info = {
+            "Generated by": "picasso-workflow : identify",
+            "Box Size": parameters["box_size"],
+            "Min. Net Gradient": parameters["min_gradient"],
+            "parameters": parameters,
+        }
+        self.info = self.info + [new_info]
+
         return parameters, results
 
     def _plot_ids_vs_frame(self, filename):
@@ -613,6 +626,21 @@ def localize(self, i, parameters, results):
                 pars["filename"]
             )
 
+        # add info
+        localize_info = {
+            "Generated by": "Picasso Localize",
+            "ROI": None,
+            "Box Size": parameters["box_size"],
+            # "Min. Net Gradient": min_net_gradient,
+            # "Convergence Criterion": convergence,
+            # "Max. Iterations": max_iterations,
+            "Pixelsize": self.analysis_config["camera_info"].get("pixelsize"),
+            "Fit method": "gausslq",
+            "Wrapped by": "picasso-workflow : localize",
+            "parameters": parameters,
+        }
+        self.info = self.info + [localize_info]
+
         # save locs
         if pars := parameters.get("save_locs"):
             if "filename" in pars.keys():
@@ -804,6 +832,13 @@ def undrift_rcc(self, i, parameters, results):
                 results["filepath_plot"], parameters["dimensions"]
             )
 
+        # add info
+        new_info = {
+            "Generated by": "picasso-workflow : undrift_rcc",
+            "parameters": parameters,
+        }
+        self.info = self.info + [new_info]
+
         # save locs
         if pars := parameters.get("save_locs"):
             if "filename" in pars.keys():
@@ -966,6 +1001,7 @@ def density(self, i, parameters, results):
         )
         density_info = {
             "Generated by": "Picasso Density",
+            "Wrapped by": "picasso-workflow : density",
             "Radius": parameters["radius"],
         }
         self.info.append(density_info)
@@ -1000,6 +1036,7 @@ def dbscan(self, i, parameters, results):
             "Generated by": "Picasso DBSCAN",
             "Radius": radius,
             "Minimum local density": min_density,
+            "Wrapped by": "picasso-workflow : dbscan",
         }
         self.info.append(dbscan_info)
         filepath = os.path.join(results["folder"], "locs_dbscan.hdf5")
@@ -1041,6 +1078,7 @@ def hdbscan(self, i, parameters, results):
             "Generated by": "Picasso HDBSCAN",
             "Min. cluster": min_cluster,
             "Min. samples": min_samples,
+            "Wrapped by": "picasso-workflow : hdbscan",
         }
         self.info.append(hdbscan_info)
         filepath = os.path.join(results["folder"], "locs_hdbscan.hdf5")
@@ -1096,6 +1134,7 @@ def smlm_clusterer(self, i, parameters, results):
             "Radius_z": radius_z,
             "Min locs": min_locs,
             "Basic frame analysis": basic_fa,
+            "Wrapped by": "picasso-workflow : smlm_clusterer",
         }
         self.info.append(smlm_cluster_info)
         filepath = os.path.join(results["folder"], "locs_smlm.hdf5")
@@ -1260,6 +1299,14 @@ def align_channels(self, i, parameters, results):
             picasso_outpost.plot_shift(shifts, cum_shifts, fig_filepath)
             results["fig_filepath"] = fig_filepath
 
+        # add info
+        new_info = {
+            "Generated by": "picasso-workflow : align_channels",
+            "shifts": results["shifts"],
+            "parameters": parameters,
+        }
+        self.info = self.info + [new_info]
+
         return parameters, results
 
     @module_decorator
@@ -1287,7 +1334,11 @@ def combine_channels(self, i, parameters, results):
 
         # replace the channel_locs with the one combined dataset
         self.channel_locs = [combined_locs]
-        info = self.channel_info[0] + ["Combined channels"]
+        new_info = {
+            "Generated by": "picasso-workflow : combine_channels",
+            "files combined": self.channel_tags,
+        }
+        info = self.channel_info[0] + [new_info]
         self.channel_info = [info]
         self.channel_tags = ["combined-channels"]