workflow fixes (#89)

ptychodus/api/workflow.py

@@ -26,6 +26,10 @@ def openProbe(self, filePath: Path, *, fileType: str | None = None) -> None:
     def buildProbe(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
         pass
 
+    @abstractmethod
+    def buildProbeFromSettings(self) -> None:
+        pass
+
     @abstractmethod
     def openObject(self, filePath: Path, *, fileType: str | None = None) -> None:
         pass
@@ -34,6 +38,10 @@ def openObject(self, filePath: Path, *, fileType: str | None = None) -> None:
     def buildObject(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
         pass
 
+    @abstractmethod
+    def buildObjectFromSettings(self) -> None:
+        pass
+
     @abstractmethod
     def reconstruct(self) -> None:
         pass

ptychodus/model/product/api.py

@@ -146,6 +146,21 @@ def buildProbe(self,
 
         item.setBuilder(builder)
 
+    def buildProbeFromSettings(self, index: int) -> None:
+        try:
+            item = self._repository[index]
+        except IndexError:
+            logger.warning(f'Failed to access item {index}!')
+            return
+
+        try:
+            builder = self._builderFactory.createFromSettings()
+        except KeyError:
+            logger.warning('Failed to create builder from settings!')
+            return
+
+        item.setBuilder(builder)
+
     def getOpenFileFilterList(self) -> Sequence[str]:
         return self._builderFactory.getOpenFileFilterList()
 
@@ -233,6 +248,21 @@ def buildObject(self,
 
         item.setBuilder(builder)
 
+    def buildObjectFromSettings(self, index: int) -> None:
+        try:
+            item = self._repository[index]
+        except IndexError:
+            logger.warning(f'Failed to access item {index}!')
+            return
+
+        try:
+            builder = self._builderFactory.createFromSettings()
+        except KeyError:
+            logger.warning('Failed to create builder from settings!')
+            return
+
+        item.setBuilder(builder)
+
     def getOpenFileFilterList(self) -> Sequence[str]:
         return self._builderFactory.getOpenFileFilterList()
 

ptychodus/model/workflow/api.py

@@ -38,12 +38,18 @@ def openProbe(self, filePath: Path, *, fileType: str | None = None) -> None:
     def buildProbe(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
         self._probeAPI.buildProbe(self._productIndex, builderName, builderParameters)
 
+    def buildProbeFromSettings(self) -> None:
+        self._probeAPI.buildProbeFromSettings(self._productIndex)
+
     def openObject(self, filePath: Path, *, fileType: str | None = None) -> None:
         self._objectAPI.openObject(self._productIndex, filePath, fileType=fileType)
 
     def buildObject(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
         self._objectAPI.buildObject(self._productIndex, builderName, builderParameters)
 
+    def buildObjectFromSettings(self) -> None:
+        self._objectAPI.buildObjectFromSettings(self._productIndex)
+
     def reconstruct(self) -> None:
         logger.debug(f'Execute Workflow: index={self._productIndex}')
         self._executor.runFlow(self._productIndex)

ptychodus/ptychodus_bdp.py

@@ -45,6 +45,7 @@ def main() -> int:
     parser.add_argument(
         '-c',
         '--comment',
+        default='',
         help='data product comment',
     )
     parser.add_argument(
@@ -214,6 +215,8 @@ def main() -> int:
             exposureTimeInSeconds=args.exposure_time_s,
         )
         workflowProductAPI.openScan(Path(args.scan_file_path.name))
+        workflowProductAPI.buildProbeFromSettings()
+        workflowProductAPI.buildObjectFromSettings()
 
         stagingDir = args.output_directory
         stagingDir.mkdir(parents=True, exist_ok=True)