update some minor config changes

Author: zain-sohail

src/sed/config/flash_example_config.yaml

@@ -217,8 +217,7 @@ dataframe:
 
 # metadata collection from scicat
 # metadata:
-#   scicat_url: <URL>
-#   scicat_token: <TOKEN>
+#   archiver_url: <URL>
 
 # The nexus collection routine shall be finalized soon for both instruments
 nexus:

src/sed/config/lab_example_config.yaml

@@ -102,7 +102,7 @@ dataframe:
     #   format: per_file
     #   dataset_key: "/uncategorised/FLASH.DIAG/TIMINGINFO/TIME1.BUNCH_FIRST_INDEX.1/time"
     # event key
-    numEvents:
+    index:
       format: per_file
       dataset_key: /DLD/NumOfEvents
     # detector x position
@@ -156,11 +156,10 @@ dataframe:
 
 # metadata collection from scicat
 # metadata:
-#   scicat_url: <URL>
-#   scicat_token: <TOKEN>
+#   archiver_url: <URL>
 
 # The nexus collection routine shall be finalized soon for both instruments
 # nexus:
-#   reader: "flash"
+#   reader: "mpes"
 #   definition: "NXmpes"
-#   input_files: ["NXmpes_config_HEXTOF_light.json"]
+#   input_files: ["NXmpes_config-HEXTOF.json"]

src/sed/loader/flash/dataframe.py

@@ -14,9 +14,9 @@
 import numpy as np
 import pandas as pd
 
+from sed.core.logging import setup_logging
 from sed.loader.flash.utils import get_channels
 from sed.loader.flash.utils import InvalidFileError
-from sed.core.logging import setup_logging
 
 logger = setup_logging("flash_dataframe_creator")
 
@@ -434,7 +434,7 @@ def df_train(self) -> pd.DataFrame:
             dataset = self.get_dataset_array(channel)
             # Electron and pulse resolved MultiIndex is created. Since this is train data,
             # the electron and pulse index is always 0
-            index = np.cumsum([0, *self.get_dataset_array("numEvents")[:-1]])
+            index = np.cumsum([0, *self.get_dataset_array("index")[:-1]])
             # Auxiliary dataset (which is stored in the same dataset as other DLD channels)
             # contains multiple channels inside. Even though they are resolved per train,
             # they come in pulse format, so the extra values are sliced and individual channels are

src/sed/loader/flash/utils.py

@@ -58,9 +58,8 @@ def get_channels(
         # Get the available channels excluding 'pulseId'.
         available_channels = list(channel_dict.keys())
         # pulse alias is an index and should not be included in the list of channels.
-        # Remove specified channels if they are present in available_channels.
-        channels_to_remove = ["pulseId", "numEvents"]
-        for channel in channels_to_remove:
+        # Remove index channels if they are present in available_channels.
+        for channel in index_list:
             if channel in available_channels:
                 available_channels.remove(channel)