add mono photon energy calculator

sed/config/flash_example_config.yaml

@@ -87,18 +87,19 @@ dataframe:
   #   slice: if the group contains multidim data, where to slice
 
   channels:
-    # pulse ID is a necessary channel for using the loader.
-    pulseId:
+    timeStamp:
+      format: per_train
+      group_name: "/uncategorised/FLASH.DIAG/TIMINGINFO/TIME1.BUNCH_FIRST_INDEX.1/"
+    pulseId:  # pulse ID is a necessary channel for using the loader.
       format: per_electron
       group_name: "/uncategorised/FLASH.EXP/HEXTOF.DAQ/DLD1/"
       slice: 2
-
-    dldPosX:
+    # DLD channels
+    dldPosX: # x position on the DLD detector
       format: per_electron
       group_name: "/uncategorised/FLASH.EXP/HEXTOF.DAQ/DLD1/"
       slice: 1
-
-    dldPosY:
+    dldPosY: # x position on the DLD detector
       format: per_electron
       group_name: "/uncategorised/FLASH.EXP/HEXTOF.DAQ/DLD1/"
       slice: 0
@@ -108,10 +109,8 @@ dataframe:
       format: per_electron
       group_name: "/uncategorised/FLASH.EXP/HEXTOF.DAQ/DLD1/"
       slice: 3
-
-    # The auxillary channel has a special structure where the group further contains
-    # a multidim structure so further aliases are defined below
-    dldAux:
+    dldAux: # The auxillary channel has a special structure where the group further contains
+            # a multidim structure so further aliases are defined below
       format: per_pulse
       group_name: "/uncategorised/FLASH.EXP/HEXTOF.DAQ/DLD1/"
       slice: 4
@@ -123,6 +122,49 @@ dataframe:
         cryoTemperature: 4
         sampleTemperature: 5
         dldTimeBinSize: 15
+    # FEL channels
+    gmdBda: # in uJ per pulse
+      format: per_pulse
+      group_name: "/FL1/Photon Diagnostic/GMD/Average energy/energy BDA/"
+      slice: 0
+    gmdPosh: # verrical position of the FEL
+      format: per_pulse
+      group_name: "/FL1/Photon Diagnostic/GMD/Average energy/energy BDA/"
+      slice: 2
+    gmdPosv: # horizontal position of the FEL
+      format: per_pulse
+      group_name: "/FL1/Photon Diagnostic/GMD/Average energy/energy BDA/"
+      slice: 3
+    bam: # Here we use the DBC2 BAM as the "normal" one is broken.
+        format: per_pulse
+        group_name: "/uncategorised/FLASH.SDIAG/BAM.DAQ/FL0.DBC2.ARRIVAL_TIME.ABSOLUTE.SA1.COMP/"
+    monochromatorPhotonEnergy: # single value. to be changed
+      format: per_train
+      group_name: "/FL1/Beamlines/PG/Monochromator/monochromator photon energy/"
+    monoDelta1:
+      format: per_train
+      group_name: "/FL1/Beamlines/PG/Monochromator/ADC.PGM2/"
+      slice: 0
+    monoDelta2:
+      format: per_train
+      group_name: "/FL1/Beamlines/PG/Monochromator/ADC.PGM2/"
+      slice: 1
+    monoMirrorAngle:
+      format: per_train
+      group_name: "/FL1/Beamlines/PG/Monochromator/ADC.PGM2/"
+      slice: 2
+    monoGratingAngle:
+      format: per_train
+      group_name: "/FL1/Beamlines/PG/Monochromator/ADC.PGM2/"
+      slice: 3
+
+    # Optical laser channels
+    delayStage:
+      format: per_train
+      group_name: "/zraw/FLASH.SYNC/LASER.LOCK.EXP/F1.PG.OSC/FMC0.MD22.1.ENCODER_POSITION.RD/dGroup/"
+    opticalDiode:
+      format: per_pulse
+      group_name: "/zraw/FLASH.LASER/FLACPUPGLASER1.PULSEENERGY/PG2_incoupl/dGroup/"
 
   # The prefixes of the stream names for different DAQ systems for parsing filenames
   # (Not to be changed by user)
@@ -139,6 +181,8 @@ dataframe:
   # (Not to be changed by user)
   beamtime_dir:
     pg2: "/asap3/flash/gpfs/pg2/"
+    hextof: "/asap3/fs-flash-o/gpfs/hextof/"
+    wespe: "/asap3/fs-flash-o/gpfs/wespe/"
 
 # metadata collection from scicat
 # metadata:

sed/loader/flash/loader.py

@@ -31,6 +31,7 @@
 from sed.core import dfops
 from sed.loader.base.loader import BaseLoader
 from sed.loader.flash.metadata import MetadataRetriever
+from sed.loader.utils import add_monochromator_photon_energy
 from sed.loader.utils import parse_h5_keys
 from sed.loader.utils import split_dld_time_from_sector_id
 
@@ -631,6 +632,12 @@ def create_dataframe_per_file(
             # correct the 3 bit shift which encodes the detector ID in the 8s time
             if self._config["dataframe"].get("split_sector_id_from_dld_time", False):
                 df = split_dld_time_from_sector_id(df, config=self._config)
+            mono_channels = ["delta1", "delta2"]
+            if all([channel in df.columns for channel in mono_channels]):
+                grating_density = self._config["dataframe"].get("gratingDensity", None)
+                order = self._config["dataframe"].get("order", None)
+                if grating_density is not None and order is not None:
+                    df = add_monochromator_photon_energy(df)
             return df
 
     def create_buffer_file(self, h5_path: Path, parquet_path: Path) -> Union[bool, Exception]:

sed/loader/utils.py

@@ -195,3 +195,56 @@ def split_dld_time_from_sector_id(
         types=[np.int8, np.int32],
     )
     return df
+
+
+def calculate_monochromator_photon_energy(
+    delta1: float,
+    delta2: float,
+    grating_density: int,
+    order: int,
+) -> float:
+    """
+    Calculates the photon energy of the monochromator using the grating density and order.
+
+    Args:
+        delta1 (float): The angle of the first crystal in radians.
+        delta2 (float): The angle of the second crystal in radians.
+        grating_density (int): The grating density in grooves per mm.
+        order (int): The order of the diffraction.
+
+    Returns:
+        float: The photon energy in eV.
+    """
+    alpha = 2.0 * delta1 + 90.0 - delta2
+    beta = -1.0 * delta2 - 86.0
+    num = 1e6 * (np.sin(beta / 180.0 * np.pi) + np.sin(alpha / 180.0 * np.pi))
+    den = order * grating_density
+    lambda_nm = num / den
+    hc = 1239.84
+    lambda_ev = hc / lambda_nm
+    return lambda_ev
+
+
+def add_monochromator_photon_energy(
+    df: Union[pd.DataFrame, dask.dataframe.DataFrame],
+    config: dict = None,
+) -> Union[pd.DataFrame, dask.dataframe.DataFrame]:
+    mono_channels = ["delta1", "delta2", "gratingDensity", "order"]
+    if config is None:
+        raise ValueError("config must be given.")
+    for channel in mono_channels:
+        if channel not in config["dataframe"]:
+            raise ValueError(f"config must contain {channel}.")
+    if "monoPhotonEnergy" in df.columns:
+        raise ValueError(
+            "Column monoPhotonEnergy already in dataframe. ",
+        )
+    df = df.assign(
+        monoPhotonEnergy=calculate_monochromator_photon_energy(
+            df[config["dataframe"]["delta1"]],
+            df[config["dataframe"]["delta2"]],
+            config["dataframe"]["gratingDensity"],
+            config["dataframe"]["order"],
+        ),
+    )
+    return df