Read data_collection_date from master file as start_time (#147)

src/nexgen/beamlines/ED_singla_nxs.py

@@ -14,6 +14,8 @@
 from ..nxs_write.NXmxWriter import EDNXmxFileWriter
 from ..nxs_write.write_utils import find_number_of_images
 from ..tools.ED_tools import extract_from_SINGLA_master, find_beam_centre
+from ..tools.ED_tools import extract_start_time_from_master
+from ..tools.ED_tools import extract_exposure_time_from_master
 from ..utils import coerce_to_path, find_in_dict, get_iso_timestamp, get_nexus_filename
 from .ED_params import ED_coord_system, EDSingla, EDSource
 
@@ -100,7 +102,7 @@ def singla_nexus_writer(
     if find_in_dict("start_time", params):
         start_time = get_iso_timestamp(params["start_time"])
     else:
-        start_time = None
+        start_time = extract_start_time_from_master(master_file)
 
     # Update source if new info passed
     source = EDSource
@@ -145,6 +147,13 @@ def singla_nexus_writer(
     det_axes = EDSingla.det_axes
     det_axes[0].start_pos = det_distance
 
+    if not exp_time:
+        logger.warning("Exposure time not set, trying to read it from the master file.")
+        exp_time = extract_exposure_time_from_master(master_file)
+
+    if not exp_time:
+        raise ValueError("Exposure time not provided. No 'count_time' in the master file.")
+
     # Define detector
     detector = Detector(
         det_params,

src/nexgen/tools/ED_tools.py

@@ -10,7 +10,12 @@
 import h5py
 import hdf5plugin  # noqa: F401
 import numpy as np
+from datetime import datetime
 from numpy.typing import ArrayLike
+import logging
+
+logger = logging.getLogger("nexgen.EDtools.Singla")
+logger.setLevel(logging.DEBUG)
 
 
 class SinglaMaster:
@@ -123,7 +128,7 @@ def get_exposure_time(self) -> float:
         _loc = [obj for obj in self.walk if "count_time" in obj]
         if len(_loc) == 0:
             return None
-        return self.__getitem__(_loc[0])[()]
+        return float(self.__getitem__(_loc[0])[()])
 
     def get_photon_energy(self) -> float:
         _loc = [obj for obj in self.walk if "photon_energy" in obj]
@@ -143,6 +148,65 @@ def get_software_version(self) -> bytes:
             return None
         return self.__getitem__(_loc[0])[()]
 
+    def get_data_collection_date(self) -> str:
+        _loc = [obj for obj in self.walk if "data_collection_date" in obj]
+        if len(_loc) == 0:
+            return None
+        else:
+            collection_date = str(self.__getitem__(_loc[0])[()])[2:21]
+            collection_date = datetime.strptime(collection_date,
+                                                '%Y-%m-%dT%H:%M:%S')
+            return collection_date
+
+
+def extract_exposure_time_from_master(master: Path | str) -> float:
+    """
+    Extracts `count_time` from the master file
+
+    Args:
+        master (Path | str): Path to Singla master file.
+
+    Returns:
+        exposure time (float): In the master file this
+        is recorded as `count_time`.
+    """
+
+    if SinglaMaster.isDectrisSingla(master) is False:
+        logger.warning(f"The file {master} is the wrong format.")
+        return
+
+    exposure_time = None
+
+    with h5py.File(master, "r") as fh:
+        singla = SinglaMaster(fh)
+        exposure_time = singla.get_exposure_time()
+
+    return exposure_time
+
+
+def extract_start_time_from_master(master: Path | str) -> datetime:
+    """
+    Extracts `data_collection_date` from the master file
+
+    Args:
+        master (Path | str): Path to Singla master file.
+
+    Returns:
+        data collection date: Datetime object.
+    """
+
+    if SinglaMaster.isDectrisSingla(master) is False:
+        logger.warning(f"The file {master} is the wrong format.")
+        return
+
+    start_time = None
+
+    with h5py.File(master, "r") as fh:
+        singla = SinglaMaster(fh)
+        start_time = singla.get_data_collection_date()
+
+    return start_time
+
 
 def extract_from_SINGLA_master(master: Path | str) -> Dict[str, Any]:
     """
@@ -155,10 +219,6 @@ def extract_from_SINGLA_master(master: Path | str) -> Dict[str, Any]:
     Returns:
         Dict[str, Any]: Dictionary of information relative to the detector.
     """
-    import logging
-
-    logger = logging.getLogger("nexgen.EDtools.Singla")
-    logger.setLevel(logging.DEBUG)
 
     if SinglaMaster.isDectrisSingla(master) is False:
         logger.warning(f"The file {master} is the wrong format.")