Merge branch 'main' into CI-playground

CHANGELOG.md

@@ -2,12 +2,13 @@
 
 
 
-## 0.#.#
+## 0.7.3
 
 ### Added
 - Added possibility to write `end_time_estimated` field in NXmxWriter and refactored `write_NXdatetime`.
 - A small utility to write a nexus file for electron diffraction and a new command line tool for SINGLA without phil.
 - Choice to avoid using the meta file for I19-2 data, as long as all relevant information is passed.
+- Utilities to extract collection start time and exposure time from singla master file for ED. 
 
 ### Changed
 - (Temporary) Write a soft link for /entry/instrument/detector/detector_z in NXdetector, for compatibility with autoPROC.

src/nexgen/beamlines/ED_singla_nxs.py

@@ -13,9 +13,13 @@
 from ..nxs_utils.ScanUtils import calculate_scan_points
 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 ..utils import (coerce_to_path, find_in_dict, get_iso_timestamp,
-                     get_nexus_filename)
+from ..tools.ED_tools import (
+    extract_detector_info_from_master,
+    extract_exposure_time_from_master,
+    extract_start_time_from_master,
+    find_beam_centre,
+)
+from ..utils import coerce_to_path, find_in_dict, get_iso_timestamp, get_nexus_filename
 from .ED_params import ED_coord_system, EDSingla, EDSource
 
 logger = logging.getLogger("nexgen.EDNeXusWriter")
@@ -101,13 +105,13 @@ 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
     if find_in_dict("new_source_info", params):
         logger.warning("Updating source information.")
-        for k, v in params["new_source_info"].keys():
+        for k, v in params["new_source_info"].items():
             source.__setattr__(k, v)
             logger.info(f"Source {k} now set to {v}.")
     logger.info(source.__repr__())
@@ -128,7 +132,7 @@ def singla_nexus_writer(
     logger.info(
         "Looking through Dectris master file to extract at least mask and flatfield."
     )
-    det_info = extract_from_SINGLA_master(master_file)
+    det_info = extract_detector_info_from_master(master_file)
     det_params.constants.update(det_info)
     # If beam_centre not passed, define it
     if not find_in_dict("beam_center", params) or params["beam_center"] is None:
@@ -146,6 +150,15 @@ 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,
@@ -181,7 +194,7 @@ def singla_nexus_writer(
     logger.info(goniometer.__repr__())
 
     vds_writer = (
-        "dataset" if not find_in_dict("vds_writer", params) else params["vds_wrter"]
+        "dataset" if not find_in_dict("vds_writer", params) else params["vds_writer"]
     )
 
     # Start writing

src/nexgen/command_line/ED_nexus.py

@@ -134,7 +134,7 @@ def write_from_SINGLA_with_phil(args):
     # Find scan axis in parsed values
     scan_idx = [
         n
-        for n in len(params.goniometer.axes)
+        for n in range(len(params.goniometer.axes))
         if params.goniometer.types[n] == "rotation"
     ][0]
     scan_info = [

src/nexgen/tools/ED_tools.py

@@ -3,6 +3,8 @@
 """
 from __future__ import annotations
 
+import logging
+from datetime import datetime
 from functools import cached_property
 from pathlib import Path
 from typing import Any, Dict, List, Tuple
@@ -12,6 +14,9 @@
 import numpy as np
 from numpy.typing import ArrayLike
 
+logger = logging.getLogger("nexgen.EDtools.Singla")
+logger.setLevel(logging.DEBUG)
+
 
 class SinglaMaster:
     """
@@ -143,8 +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_from_SINGLA_master(master: Path | str) -> Dict[str, Any]:
+def extract_exposure_time_from_master(master: Path | str) -> float:
+    """
+    Extracts the exposure time from the count_time field in the master file.
+
+    Args:
+        master (Path | str): Path to Singla master file.
+
+    Returns:
+        exposure_time (float): Exposure time, in seconds.
+    """
+
+    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 start_time from the data_collection_date field of the master file.
+
+    Args:
+        master (Path | str): Path to Singla master file.
+
+    Returns:
+        start_time (datetime): Collection start time, as 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_detector_info_from_master(master: Path | str) -> Dict[str, Any]:
     """
     Extracts mask, flatfield and any other information relative to the detector \
     from a Singla master file.
@@ -155,10 +217,6 @@ 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.")

tests/tools/test_tools_for_ED.py

@@ -1,4 +1,5 @@
 import tempfile
+from datetime import datetime
 
 import h5py
 import numpy as np
@@ -8,7 +9,9 @@
 from nexgen.tools.ED_tools import (
     SinglaMaster,
     centroid_max,
-    extract_from_SINGLA_master,
+    extract_detector_info_from_master,
+    extract_exposure_time_from_master,
+    extract_start_time_from_master,
     find_beam_centre,
 )
 
@@ -39,6 +42,10 @@
 def dummy_singla_master_file():
     test_hdf_file = tempfile.NamedTemporaryFile(suffix=".h5", delete=True)
     with h5py.File(test_hdf_file, "w") as test_master_file:
+        test_master_file["/entry/instrument/detector/count_time"] = 0.1
+        test_master_file[
+            "/entry/instrument/detector/detectorSpecific/data_collection_date"
+        ] = "2023-12-06T10:30:42.039+02:00"
         test_master_file["/entry/instrument/detector/description/"] = b"Dectris Singla"
         test_master_file["/entry/instrument/detector/pixel_mask_applied"] = False
         test_master_file[
@@ -56,7 +63,7 @@ def test_isSingla_master_file(dummy_singla_master_file):
 
 
 def test_get_mask_and_flatfield_from_singla_master_file(dummy_singla_master_file):
-    D = extract_from_SINGLA_master(dummy_singla_master_file.name)
+    D = extract_detector_info_from_master(dummy_singla_master_file.name)
     assert "pixel_mask" in D.keys() and "flatfield" in D.keys()
     assert D["pixel_mask"] is None
     assert D["pixel_mask_applied"] == 0
@@ -65,12 +72,24 @@ def test_get_mask_and_flatfield_from_singla_master_file(dummy_singla_master_file
 
 
 def test_get_software_version_from_singla_master_file(dummy_singla_master_file):
-    D = extract_from_SINGLA_master(dummy_singla_master_file.name)
+    D = extract_detector_info_from_master(dummy_singla_master_file.name)
     assert "software_version" in D.keys()
-    assert type(D["software_version"]) is bytes
+    assert isinstance(D["software_version"], bytes)
     assert D["software_version"].decode() == "0.0.0"
 
 
+def test_get_exposure_time_from_singla_master_file(dummy_singla_master_file):
+    exp_time = extract_exposure_time_from_master(dummy_singla_master_file.name)
+    assert isinstance(exp_time, float)
+    assert exp_time == 0.1
+
+
+def test_get_collection_start_time_from_singla_master_file(dummy_singla_master_file):
+    start_time = extract_start_time_from_master(dummy_singla_master_file.name)
+    assert isinstance(start_time, datetime)
+    assert start_time == datetime.fromisoformat("2023-12-06T10:30:42")
+
+
 def test_get_nimages_and_triggers(dummy_singla_master_file):
     with h5py.File(dummy_singla_master_file.name, "r") as fh:
         master = SinglaMaster(fh)
@@ -110,6 +129,6 @@ def test_find_beam_center(dummy_singla_master_file):
     beam_center = find_beam_centre(
         dummy_singla_master_file.name, test_img_hdf_file.name
     )
-    assert type(beam_center) is tuple
+    assert isinstance(beam_center, tuple)
     assert beam_center[0] is not None
     assert beam_center[1] is not None