nena debugs

jungmannlab · Apr 9, 2024 · de9f58b · de9f58b
1 parent b30017f
commit de9f58b
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Showing 2 changed files with 52 additions and 6 deletions.
diff --git a/picasso_workflow/analyse.py b/picasso_workflow/analyse.py
@@ -730,16 +730,52 @@ def summarize_dataset(self, i, parameters, results):
         for meth, meth_pars in parameters["methods"].items():
             if meth.lower() == "nena":
                 try:
-                    res, best_vals = postprocess.nena(self.locs, self.info)
-                    results["nena"] = {"res": str(res), "best_vals": best_vals}
-                except ValueError:
+                    res, best_val = postprocess.nena(self.locs, self.info)
+                    fp_plot = os.path.join(results["folder"], "nena.png")
+                    self._plot_nena(res, fp_plot)
+                    all_best_vals = {
+                        "a": res.best_values["a"],
+                        "s": res.best_values["s"],
+                        "ac": res.best_values["ac"],
+                        "dc": res.best_values["dc"],
+                        "sc": res.best_values["sc"],
+                    }
+                    results["nena"] = {
+                        "res": str(all_best_vals),
+                        "chisqr": res.chisqr,
+                        "NeNa": (
+                            f"{best_val:.3f} px;"
+                            + f" {130*best_val:.3f} nm "
+                            + "(assuming 130nm pixel size)"
+                        ),
+                        "filepath_plot": fp_plot,
+                    }
+                except ValueError as e:
+                    logger.error(e)
                     results["nena"] = {"res": "Fitting Error", "best_vals": ""}
+                except Exception as e:
+                    logger.error(e)
+                    results["nena"] = {
+                        "res": str(e.msg),
+                        "best_vals": "Error.",
+                    }
             else:
                 raise NotImplementedError(
                     f"Description method {meth} not implemented."
                 )
         return parameters, results
 
+    def _plot_nena(self, nena_result, filepath_plot):
+        fig, ax = plt.subplots()
+        d = nena_result.userkws["d"]
+        ax.set_title("Next frame neighbor distance histogram")
+        ax.plot(d, nena_result.data, label="Data")
+        ax.plot(d, nena_result.best_fit, label="Fit")
+        ax.set_xlabel("Distance [px]")
+        ax.set_ylabel("Counts")
+        ax.legend(loc="best")
+        fig.savefig(filepath_plot)
+
     @module_decorator
     def save_single_dataset(self, i, parameters, results):
         """Saves the locs and info of a single dataset; makes loading

diff --git a/picasso_workflow/confluence.py b/picasso_workflow/confluence.py
@@ -250,7 +250,7 @@ def undrift_rcc(self, i, pars_undrift, res_undrift):
             self.report_page_name, self.report_page_id, text
         )
 
-        if driftimg_fn := pars_undrift.get("filepath_plot"):
+        if driftimg_fn := res_undrift.get("filepath_plot"):
             self.ci.upload_attachment(self.report_page_id, driftimg_fn)
             self.ci.update_page_content_with_image_attachment(
                 self.report_page_name,
@@ -289,12 +289,22 @@ def summarize_dataset(self, i, parameters, results):
                 text += f"""
                     <p>NeNa</p>
                     <ul>
-                    <li>Best Values: {str(meth_res.get('best_vals'))}</li>
-                    <li>Result: {str(meth_res.get('res'))}</li>
+                    <li>NeNa value: {str(meth_res.get('NeNa'))}</li>
+                    <li>Best Fit Values: {str(meth_res.get('res'))}</li>
+                    <li>Chi Square: {str(meth_res.get('chisqr'))}</li>
                     </ul>"""
+                if fp_nena := meth_res.get("filepath_plot"):
+                    self.ci.upload_attachment(self.report_page_id, fp_nena)
+                    _, fn_nena = os.path.split(fp_nena)
+                    text += (
+                        "<ul><ac:image><ri:attachment "
+                        + f'ri:filename="{fn_nena}" />'
+                        + "</ac:image></ul>"
+                    )
         text += """
         </ac:layout-cell></ac:layout-section></ac:layout>
         """
+        logger.debug("description text: " + text)
         self.ci.update_page_content(
             self.report_page_name, self.report_page_id, text
         )