MNT #13 work-in-progress

instrument/callbacks/nexus_data_file_writer.py

@@ -8,27 +8,69 @@
 
 __all__ = ["nxwriter"]
 
+import h5py
 from apstools.callbacks import NXWriterAPS
 
 from .._iconfig import iconfig
-from ..framework.initialize import RE
+# from ..framework.initialize import RE
 
 
 class MyNXWriter(NXWriterAPS):
+    """
+    Modify the default behavior of NXWriter for XPCS.
+    """
+
     def get_sample_title(self):
         """
         Get the title from the metadata or modify the default.
 
         default title: S{scan_id}-{plan_name}-{short_uid}
         """
         try:
-            title = self.metadata["title"]
+            title = f'S{self.scan_id:05d}-{self.metadata["title"]}'
         except KeyError:
             # title = super().get_sample_title()  # the default title
             title = f"S{self.scan_id:05d}-{self.plan_name}-{self.uid[:7]}"
         return title
 
-    # FIXME: do not copy the image data to this file
+    def write_stream_external(self, parent, d, subgroup, stream_name, k, v):
+        """
+        Modify the default behavior of NXWriter.  Don't copy the image.
+
+        Create an external file link to the image file data.
+        Do not delay by waiting for the image file to close, then copying
+        the image data to the one NeXus file.
+        """
+        resource_id = self.get_unique_resource(d)
+        fname = self.getResourceFile(resource_id)
+
+        h5addr = "/entry/data/data"  # NeXus default data address.
+        # TODO: Which file path to use when making the external link?
+        ds = h5py.ExternalLink(str(fname), h5addr)  # TODO: check the path
+        subgroup["value"] = ds
+        # FIXME: attrs don't work here, refactor
+        # ds.attrs["image_file"] = str(fname)
+        # ds.attrs["image_address"] = h5addr
+        # ds.attrs["bluesky_resource_id"] = resource_id
+        # ds.attrs["shape"] = v.get("shape", "")
+        # ds.attrs["target"] = ds.name
+
+    def get_unique_resource(self, datum_id_list):
+        # count number of unique resources (expect only 1)
+        resource_id_list = []
+        for datum_id in datum_id_list:
+            resource_id = self.externals[datum_id]["resource"]
+            if resource_id not in resource_id_list:
+                resource_id_list.append(resource_id)
+        if len(resource_id_list) != 1:
+            # fmt: off
+            raise ValueError(
+                f"{len(resource_id_list)}"
+                f" unique resource UIDs: {resource_id_list}"
+            )
+            # fmt: on
+        return resource_id_list[0]
+
     # TODO: include the metadata like we did previously
     #   old_code/spec_support/APS_DM_8idi.py starting at line ~310
     #   Use a separate stream named "ad_metadata"
@@ -38,7 +80,7 @@ def get_sample_title(self):
 
 
 nxwriter = MyNXWriter()  # create the callback instance
-RE.subscribe(nxwriter.receiver)  # subscribe to the RunEngine
+#RE.subscribe(nxwriter.receiver)  # subscribe to the RunEngine
 
 warn_missing = iconfig.get("NEXUS_WARN_MISSING_CONTENT", False)
 nxwriter.warn_on_missing_content = warn_missing