included ub conf into spice logs

Author: Bing Li

src/tavi/data/nxdict.py

@@ -5,6 +5,7 @@
 from pathlib import Path
 from typing import Optional
 
+import h5py
 import numpy as np
 
 from tavi.data.spice_reader import _create_spicelogs, read_spice_datafile
@@ -109,13 +110,21 @@ def add_attribute(self, key: str, attr):
 
 def _formatted_spicelogs(spicelogs: dict) -> NXentry:
     """Format SPICE logs into NeXus dict"""
-    formatted_spicelogs = NXentry(NX_class="NXcollection", EX_required="false")
+    ub_conf = spicelogs.pop("ub_conf")
+    ub_file_path = ub_conf.pop("file_path")
+    formatted_ub_conf = NXentry(file_path=ub_file_path, NX_class="NXcollection", EX_required="false")
+    for entry_key, entry_data in ub_conf.items():
+        formatted_ub_conf.add_dataset(key=entry_key, ds=NXdataset(ds=entry_data))
+
     metadata = spicelogs.pop("metadata")
+    formatted_spicelogs = NXentry(ub_conf=formatted_ub_conf, NX_class="NXcollection", EX_required="false")
+
     for attr_key, attr_entry in metadata.items():
         formatted_spicelogs.add_attribute(attr_key, attr_entry)
 
     for entry_key, entry_data in spicelogs.items():
         formatted_spicelogs.add_dataset(key=entry_key, ds=NXdataset(ds=entry_data))
+
     return formatted_spicelogs
 
 
@@ -280,6 +289,13 @@ def spice_scan_to_nxdict(
         EX_required="true",
     )
     nxsample.add_dataset(key="Pt.", ds=NXdataset(ds=spicelogs.get("Pt."), type="NX_INT"))
+    #  UB info
+    nxsample.add_dataset(
+        key="orientation_matrix",
+        ds=NXdataset(ds=metadata.get("ubmatrix"), type="NX_FLOAT", EX_required="true", units="NX_DIMENSIONLESS"),
+    )
+    # nxsample.add_dataset(key="ub_conf", ds=NXdataset(ds=metadata["ubconf"].split(".")[0], type="NX_CHAR"))
+    nxsample.add_dataset(key="plane_normal", ds=NXdataset(ds=metadata.get("plane_normal"), type="NX_FLOAT"))
 
     # Motor angles
     nxsample.add_dataset(key="s1", ds=NXdataset(ds=spicelogs.get("s1"), type="NX_FLOAT", units="degrees"))
@@ -289,14 +305,6 @@ def spice_scan_to_nxdict(
     nxsample.add_dataset(key="stu", ds=NXdataset(ds=spicelogs.get("stu"), type="NX_FLOAT", units="degrees"))
     nxsample.add_dataset(key="stl", ds=NXdataset(ds=spicelogs.get("stl"), type="NX_FLOAT", units="degrees"))
 
-    # UB info
-    nxsample.add_dataset(
-        key="orientation_matrix",
-        ds=NXdataset(ds=metadata.get("ubmatrix"), type="NX_FLOAT", EX_required="true", units="NX_DIMENSIONLESS"),
-    )
-    nxsample.add_dataset(key="ub_conf", ds=NXdataset(ds=metadata["ubconf"].split(".")[0], type="NX_CHAR"))
-    nxsample.add_dataset(key="plane_normal", ds=NXdataset(ds=metadata.get("plane_normal"), type="NX_FLOAT"))
-
     # ---------------------------------------- sample environment ---------------------------------------------
 
     # TODO all sample environment variable names needed!
@@ -381,14 +389,14 @@ def spice_data_to_nxdict(
     for path_to_scan_file in scan_list:
         *_, file_name = path_to_scan_file.split("/")
         *_, scan_dat = file_name.split("_")
-        scan_num, _ = scan_dat.split(".")
+        scan_name, _ = scan_dat.split(".")
 
         nxentry = spice_scan_to_nxdict(
             path_to_scan_file,
             path_to_instrument_json,
             path_to_sample_json,
         )
         nxentry["attrs"].update({"dataset_name": dataset_name})
-        nexus_dict.update({scan_num: nxentry})
+        nexus_dict.update({scan_name: nxentry})
 
     return nexus_dict

src/tavi/data/nxdict_backup.py

@@ -217,8 +217,8 @@ def to_nexus(self, path_to_nexus: str, name="scan") -> None:
             scan_grp = nexus_file.require_group(name + "/")
             NexusEntry._write_recursively(self, scan_grp)
             # create soft link for data
-            def_y = nexus_file["scan0034"]["data"].attrs["signal"]
-            def_x = nexus_file["scan0034"]["data"].attrs["axes"]
+            def_y = nexus_file[name]["data"].attrs["signal"]
+            def_x = nexus_file[name]["data"].attrs["axes"]
             path_y = _find_val_path(def_y, nexus_file)
             path_x = _find_val_path(def_x, nexus_file)