Add tests (DiamondLightSource#153)

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 +13,12 @@
 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 ..tools.ED_tools import extract_start_time_from_master
-from ..tools.ED_tools import extract_exposure_time_from_master
+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
 
@@ -129,7 +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:
@@ -152,7 +155,9 @@ def singla_nexus_writer(
         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.")
+        raise ValueError(
+            "Exposure time not provided. No 'count_time' in the master file."
+        )
 
     # Define detector
     detector = Detector(

src/nexgen/tools/ED_tools.py

@@ -3,16 +3,16 @@
 """
 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
 
 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)
@@ -128,7 +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 float(self.__getitem__(_loc[0])[()])
+        return self.__getitem__(_loc[0])[()]
 
     def get_photon_energy(self) -> float:
         _loc = [obj for obj in self.walk if "photon_energy" in obj]
@@ -154,21 +154,19 @@ def get_data_collection_date(self) -> str:
             return None
         else:
             collection_date = str(self.__getitem__(_loc[0])[()])[2:21]
-            collection_date = datetime.strptime(collection_date,
-                                                '%Y-%m-%dT%H:%M:%S')
+            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
+    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): In the master file this
-        is recorded as `count_time`.
+        exposure_time (float): Exposure time, in seconds.
     """
 
     if SinglaMaster.isDectrisSingla(master) is False:
@@ -186,13 +184,13 @@ def extract_exposure_time_from_master(master: Path | str) -> float:
 
 def extract_start_time_from_master(master: Path | str) -> datetime:
     """
-    Extracts `data_collection_date` from the master file
+    Extracts start_time from the data_collection_date field of the master file.
 
     Args:
         master (Path | str): Path to Singla master file.
 
     Returns:
-        data collection date: Datetime object.
+        start_time (datetime): Collection start time, as datetime object.
     """
 
     if SinglaMaster.isDectrisSingla(master) is False:
@@ -208,7 +206,7 @@ def extract_start_time_from_master(master: Path | str) -> datetime:
     return start_time
 
 
-def extract_from_SINGLA_master(master: Path | str) -> Dict[str, Any]:
+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.

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