Allow for a different data entry key

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
   hooks:
     - id: ruff
       name: Run ruff
-      stages: [commit]
+      stages: [pre-commit]
       language: system
       entry: ruff check
       types: [python]

src/nexgen/beamlines/I19_2_nxs.py

@@ -229,6 +229,7 @@ def eiger_writer(
     n_frames: int | None = None,
     vds_offset: int = 0,
     notes: dict[str, Any] | None = None,
+    data_entry_key: str = "data",
 ):
     """
     A function to call the NXmx nexus file writer for Eiger 2X 4M detector.
@@ -248,6 +249,8 @@ def eiger_writer(
         vds_offset (int, optional): Start index for the vds writer. Defaults to 0.
         notes (dict[str, Any], optional): Dictionary of (key, value) pairs where key represents the \
             dataset name and value its data. Defaults to None.
+        data_entry_key (str, optional): Dataset entry key in datafiles. eg. for gating mode it's data1.\
+            Defaults to data.
 
     Raises:
         ValueError: If use_meta is set to False but axes_pos and det_pos haven't been passed.
@@ -424,7 +427,11 @@ def eiger_writer(
             TR.tot_num_images,
             sample,
         )
-        NXmx_writer.write(image_filename=image_filename, start_time=timestamps[0])
+        NXmx_writer.write(
+            image_filename=image_filename,
+            start_time=timestamps[0],
+            data_entry_key=data_entry_key,
+        )
         NXmx_writer.write_vds(
             vds_offset=vds_offset,
             vds_shape=(n_frames, *detector.detector_params.image_size),
@@ -515,6 +522,7 @@ def nexus_writer(
     master_file: Path,
     timestamps: tuple[datetime, datetime] = (None, None),
     use_meta: bool = False,
+    data_entry_key: str = "data",
 ):
     """Wrapper function to gather all parameters from the beamline and kick off the nexus writer for a \
     standard experiment on I19-2.
@@ -526,6 +534,8 @@ def nexus_writer(
             Defaults to (None, None).
         use_meta (bool, optional): Eiger option only, if True use metadata from meta.h5 file. Otherwise \
             all parameters will need to be passed manually. Defaults to False.
+        data_entry_key (str, optional): Dataset entry key in datafiles. eg. for gating mode it's data1.\
+            Defaults to data.
     """
     collection_params = CollectionParams(**params)
     wdir = master_file.parent
@@ -592,6 +602,7 @@ def nexus_writer(
                 collection_params,
                 timestamps,
                 use_meta,
+                data_entry_key=data_entry_key,
             )
         case DetectorName.TRISTAN:
             tristan_writer(

src/nexgen/command_line/I19_2_cli.py

@@ -142,6 +142,7 @@ def nexgen_writer(args):
             master_file,
             (_start, _stop),
             args.use_meta,
+            data_entry_key=args.data_key,
         )
 
 
@@ -236,12 +237,12 @@ def nexgen_writer(args):
 )
 parser_nex.add_argument("meta_file", type=str, help="Path to _meta.h5 file.")
 parser_nex.add_argument(
-    "detector-name",
+    "detector_name",
     type=str,
     choices=["eiger", "tristan"],
     help="Detector currently in use on beamline.",
 )
-parser_nex.add_argument("exp-time", type=float, help="Exposure time, in s.")
+parser_nex.add_argument("exp_time", type=float, help="Exposure time, in s.")
 parser_nex.add_argument(
     "-n",
     "--num-imgs",
@@ -297,6 +298,12 @@ def nexgen_writer(args):
     help="Number of frames in the nexus and vds file. Only passed if different from total number \
         of images collected.",
 )
+parser_nex.add_argument(
+    "--data-key",
+    type=str,
+    default="data",
+    help="Data entry key of dataset in raw .h5 file. Defaults to data.",
+)
 parser_nex.set_defaults(func=nexgen_writer)
 
 

src/nexgen/command_line/nexus_generator.py

@@ -48,6 +48,7 @@ def _get_datafiles(filepath: Path, filename_root: str) -> list[Path]:
         for f in glob.glob(_file_template.as_posix())
         if "meta.h5" not in f
     ]
+    datafiles.sort()
     return datafiles
 
 
@@ -141,6 +142,7 @@ def write_nxmx_cli(args):
     logger.debug(f"Recorded exposure time: {detector.exp_time} s.")
 
     try:
+        entry_key = args.data_key if args.data_key else "data"
         # Aaaaaaaaaaaand write
         if params.det.mode == "images":
             writer = NXmxFileWriter(
@@ -152,7 +154,7 @@ def write_nxmx_cli(args):
                 params.instrument.attenuator,
                 num_images,
             )
-            writer.write(image_datafiles=datafiles)
+            writer.write(image_datafiles=datafiles, data_entry_key=entry_key)
             if not args.no_vds:
                 writer.write_vds(args.vds_offset)
         else:
@@ -382,6 +384,12 @@ def _parse_cli() -> argparse.ArgumentParser:
         type=str,
         help="New nexus filename if stem needs to be different from data files.",
     )
+    nxmx_parser.add_argument(
+        "--data-key",
+        type=str,
+        default="data",
+        help="Data entry key of dataset in raw .h5 file. Defaults to data.",
+    )
     nxmx_parser.set_defaults(func=write_nxmx_cli)
     demo_parser = subparsers.add_parser(
         "2",

src/nexgen/nxs_write/nxmx_writer.py

@@ -142,6 +142,7 @@ def write(
         est_end_time: datetime | str | None = None,
         write_mode: str = "x",
         add_non_standard: bool = True,
+        data_entry_key: str = "data",
     ):
         """Write the NXmx format NeXus file.
 
@@ -162,6 +163,7 @@ def write(
                 Accepts any valid h5py file opening mode. Defaults to "x".
             add_non_standard (bool, optional): Flag if non-standard NXsample fields should be added \
                 for processing to work. Defaults to True, will change in the future.
+            data_entry_key (str, optional): Dataset entry key in datafiles. Defaults to data.
         """
         metafile = self._get_meta_file(image_filename)
         if metafile:
@@ -193,10 +195,7 @@ def write(
 
             # NXdata: entry/data
             write_NXdata(
-                nxs,
-                datafiles,
-                "images",
-                list(osc.keys())[0],
+                nxs, datafiles, "images", list(osc.keys())[0], entry_key=data_entry_key
             )
 
             # NXinstrument: entry/instrument
@@ -341,6 +340,7 @@ def write(
         start_time: datetime | str | None = None,
         write_mode: str = "x",
         add_non_standard: bool = False,
+        data_entry_key: str = "data",
     ):
         """Write a NXmx-like NeXus file for event mode data collections.
 
@@ -356,6 +356,7 @@ def write(
                 Accepts any valid h5py file opening mode. Defaults to "x".
             add_non_standard (bool, optional): Flag if non-standard NXsample fields should be added \
                 for processing to work. Defaults to False.
+            data_entry_key (str, optional): Dataset entry key in datafiles. Defaults to data.
         """
         # Get metafile
         # No data files, just link to meta
@@ -381,6 +382,7 @@ def write(
                 [metafile],
                 "events",
                 list(osc.keys())[0],
+                entry_key=data_entry_key,
             )
 
             # NXinstrument: entry/instrument