fix: no None in docs, variable ref

NSLS-II-PDF · Apr 11, 2024 · 4044916 · 4044916
1 parent 0253cf5
commit 4044916
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/containers/mmm5-tax-day-compose.yaml b/containers/mmm5-tax-day-compose.yaml
@@ -15,8 +15,8 @@ services:
       - BS_AGENT_STARTUP_SCRIPT_PATH=/src/pdf-agents/pdf_agents/startup_scripts/mmm5-tax-day/gsas.py
     volumes:
       - type: bind
-        source: ../pdf_agents
-        target: /src/pdf-agents/pdf_agents
+        source: ../
+        target: /src/pdf-agents/
         read_only: true
       - type: bind
         source: /etc/bluesky/kafka.yml
@@ -53,8 +53,8 @@ services:
       - BS_AGENT_STARTUP_SCRIPT_PATH=/src/pdf-agents/pdf_agents/startup_scripts/mmm5-tax-day/kmeans-gsas.py
     volumes:
       - type: bind
-        source: ../pdf_agents
-        target: /src/pdf-agents/pdf_agents
+        source: ../
+        target: /src/pdf-agents/
         read_only: true
       - type: bind
         source: /etc/bluesky/kafka.yml

diff --git a/pdf_agents/agents.py b/pdf_agents/agents.py
@@ -100,8 +100,8 @@ def unpack_run(self, run) -> Tuple[Union[float, ArrayLike], Union[float, ArrayLi
         if self.background is not None:
             y = y - self.background[1]
 
+        ordinate = np.array(run.primary.data[self.roi_key]).flatten()
         if self.norm_region is not None:
-            ordinate = np.array(run.primary.data[self.roi_key]).flatten()
             idx_min = (
                 np.where(ordinate < self.norm_region[0])[0][-1]
                 if len(np.where(ordinate < self.norm_region[0])[0])
@@ -132,6 +132,8 @@ def unpack_run(self, run) -> Tuple[Union[float, ArrayLike], Union[float, ArrayLi
             ordinate = np.array(run.primary.data[self.roi_key]).flatten()
             idx_min = np.where(ordinate < self.roi[0])[0][-1] if len(np.where(ordinate < self.roi[0])[0]) else None
             idx_max = np.where(ordinate > self.roi[1])[0][-1] if len(np.where(ordinate > self.roi[1])[0]) else None
+        else:
+            idx_min, idx_max = None, None
 
         y = y[idx_min:idx_max]
         self._ordinate = ordinate[idx_min:idx_max]  # Update self oridnate. Should be constant unless roi changes.

diff --git a/pdf_agents/gsas.py b/pdf_agents/gsas.py
@@ -176,9 +176,9 @@ def report(self) -> Dict[str, ArrayLike]:
 
         return dict(
             data_key=self.data_key,
-            roi_key=self.roi,
-            roi=self.roi,
-            norm_region=self.norm_region,
+            roi_key=self.roi_key if self.roi_key is not None else "",
+            roi=self.roi if self.roi is not None else "",
+            norm_region=self.norm_region if self.norm_region is not None else "",
             observable_uid=self._recent_uid,
             independent_variable=self._recent_x,
             observable=self._recent_y,