Fix Incorrect Sample Shape In Added SANS Runs (#39389)

This pulls the following into `ornl-next`
* #39234
* #39365

---------

Co-authored-by: Caila Finn <47181718+cailafinn@users.noreply.github.com>

Author: peterfpeterson

Testing/Data/UnitTest/LOQ54432.raw.md5

@@ -0,0 +1 @@
+39129303843e41fa060cc4b50413ff3a

Testing/Data/UnitTest/LOQ74014.nxs.md5

@@ -0,0 +1 @@
+ee8bbab4b40dbd3d03eb7ea6978347b3

Testing/SystemTests/tests/framework/ISIS/SANS/WORKFLOWS/SANSUtilityTest.py

@@ -27,7 +27,7 @@ class SANSUtilityTest(systemtesting.MantidSystemTest):
     def runTest(self):
         # created after issue reported in #8156
         ws = Load("LOQ54432")
-        self.assertTrue("LOQ/LOQ54432.raw" in unixLikePathFromWorkspace(ws))
+        self.assertTrue("LOQ54432.raw" in unixLikePathFromWorkspace(ws))
         ws = Load("LOQ99618.RAW")
         self.assertTrue("LOQ/LOQ99618.RAW" in unixLikePathFromWorkspace(ws))
         add.add_runs(("LOQ54432", "LOQ54432"), "LOQ", ".raw")

docs/source/release/v6.13.0/SANS/Bugfixes/39106.rst

@@ -0,0 +1,2 @@
+- :ref:`ISIS_SANS_Sum_Runs_Tab-ref` in the ISIS SANS interface now maintains the sample properties
+  (shape, thickness, height, and width) of the runs in the added output file.

scripts/SANS/SANSUtility.py

@@ -813,14 +813,17 @@ def is_nexus_file(file_name):
     full_file_path = FileFinder.findRuns(file_name)
     if hasattr(full_file_path, "__iter__"):
         file_name = full_file_path[0]
-    is_nexus = True
-    try:
-        with h5.File(file_name, "r") as h5_file:
-            keys = list(h5_file.keys())
-            nexus_test = "raw_data_1" in keys or "mantid_workspace_1" in keys
-            is_nexus = True if nexus_test else False
-    except:
-        is_nexus = False
+    # quick check that is hdf5
+    is_nexus = h5.is_hdf5(file_name)
+    # fuller test looks at top level entries
+    if is_nexus:
+        try:
+            keys = []
+            with h5.File(file_name, "r") as h5_file:
+                keys = list(h5_file.keys())
+            is_nexus = bool("raw_data_1" in keys or "mantid_workspace_1" in keys)
+        except:
+            is_nexus = False
     return is_nexus
 
 

scripts/SANS/SANSadd2.py

@@ -26,6 +26,7 @@
     SaveNexusProcessed,
     UnGroupWorkspace,
 )
+from sans.common.file_information import get_geometry_information_isis_nexus, convert_to_flag
 from SANSUtility import (
     AddOperation,
     transfer_special_sample_logs,
@@ -302,7 +303,8 @@ def _make_filename(entry, ext, inst):
         filename = inst + _pad_zero(run_num, inst) + ext
     except ValueError:  # We don't have a run number, assume it's a valid filename
         filename = entry
-        dummy, ext = os.path.splitext(filename)
+        _, filename_ext = os.path.splitext(filename)
+        ext = filename_ext if filename_ext else ext
 
     return filename, ext
 
@@ -378,6 +380,13 @@ def _load_ws(entry, ext, inst, ws_name, raw_types, period=_NO_INDIVIDUAL_PERIODS
 
     if _is_type(ext, raw_types):
         LoadSampleDetailsFromRaw(InputWorkspace=ws_name, Filename=path + "/" + f_name)
+    else:
+        height, width, thickness, shape = get_geometry_information_isis_nexus(full_path)
+        sample = mtd[ws_name].sample()
+        sample.setGeometryFlag(convert_to_flag(shape))
+        sample.setHeight(height)
+        sample.setWidth(width)
+        sample.setThickness(thickness)
 
     # Change below when logs in Nexus files work  file types of .raw need their log files to be copied too
     # if isType(ext, raw_types):

scripts/SANS/sans/common/file_information.py

@@ -61,9 +61,6 @@
 HEIGHT = "height"
 THICKNESS = "thickness"
 SHAPE = "shape"
-CYLINDER = "CYLINDER"
-FLAT_PLATE = "FLAT PLATE"
-DISC = "DISC"
 GEOM_HEIGHT = "geom_height"
 GEOM_WIDTH = "geom_width"
 GEOM_THICKNESS = "geom_thickness"
@@ -304,6 +301,25 @@ def convert_to_flag(shape_string):
     return shape
 
 
+def convert_nexus_shape_to_sample_shape(nexus_shape: str) -> SampleShape | None:
+    """
+    The ISIS nexus shape format can contain a space in flat plate.
+    Handle this here for consistency with the other conversions.
+    :param nexus_shape: The shape extracted from the ISIS nexus file.
+    :return: The SampleShape version of the shape.
+    """
+    nexus_shape = nexus_shape.upper()
+    match nexus_shape:
+        case "FLAT PLATE" | "FLATPLATE":
+            return SampleShape.FLAT_PLATE
+        case "DISC":
+            return SampleShape.DISC
+        case "CYLINDER":
+            return SampleShape.CYLINDER
+        case _:
+            return None
+
+
 # ----------------------------------------------------------------------------------------------------------------------
 # Functions for ISIS Nexus
 # ----------------------------------------------------------------------------------------------------------------------
@@ -394,12 +410,12 @@ def is_raw_nexus_event_mode(file_name):
                                     |--some_group|
                                                  |--Attribute: NX_class = NXevent_data
     """
+    is_event_mode = False
     with h5.File(file_name, "r") as h5_file:
         # Open first entry
         keys = list(h5_file.keys())
         first_entry = h5_file[keys[0]]
         # Open instrument group
-        is_event_mode = False
         for value in list(first_entry.values()):
             if NX_CLASS in value.attrs and NX_EVENT_DATA == value.attrs[NX_CLASS].decode("utf-8"):
                 is_event_mode = True
@@ -423,14 +439,7 @@ def get_geometry_information_isis_nexus(file_name):
         width = float(sample[WIDTH][0])
         thickness = float(sample[THICKNESS][0])
         shape_as_string = sample[SHAPE][0].upper().decode("utf-8")
-        if shape_as_string == CYLINDER:
-            shape = SampleShape.CYLINDER
-        elif shape_as_string == FLAT_PLATE:
-            shape = SampleShape.FLAT_PLATE
-        elif shape_as_string == DISC:
-            shape = SampleShape.DISC
-        else:
-            shape = None
+        shape = convert_nexus_shape_to_sample_shape(shape_as_string)
     return height, width, thickness, shape
 
 

scripts/test/SANS/CMakeLists.txt

@@ -1,6 +1,7 @@
 pyunittest_add_test(
   ${CMAKE_CURRENT_SOURCE_DIR}
   python.SANS
+  SANSadd2Test.py
   SANSBatchModeTest.py
   SANSCentreFinderTest.py
   SANSCommandInterfaceTest.py

scripts/test/SANS/SANSadd2Test.py

@@ -0,0 +1,52 @@
+# Mantid Repository : https://github.com/mantidproject/mantid
+#
+# Copyright © 2025 ISIS Rutherford Appleton Laboratory UKRI,
+#   NScD Oak Ridge National Laboratory, European Spallation Source,
+#   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
+# SPDX - License - Identifier: GPL - 3.0 +
+
+import unittest
+from unittest.mock import patch
+
+from SANS import SANSadd2
+from SANS.sans.common.enums import SampleShape
+from mantid.simpleapi import Load
+
+
+class TestSANSAddSampleMetadata(unittest.TestCase):
+    def test_raw_files_get_correct_sample_info(self):
+        result = SANSadd2.add_runs(("LOQ54432", "LOQ54432"), "LOQ", ".raw")
+        assert result.startswith("The following file has been created:")
+        assert result.endswith("LOQ54432-add.nxs")
+
+        # load the output file and verify it has the sample information
+        ws = Load("LOQ54432-add.nxs")
+        sample = ws.sample()
+        self.assertEqual(3, sample.getGeometryFlag())
+        self.assertEqual(8.0, sample.getHeight())
+        self.assertEqual(8.0, sample.getWidth())
+        self.assertAlmostEqual(1.035, sample.getThickness())
+
+    def test_raw_files_collect_sample_info_using_alg(self):
+        with patch("SANS.SANSadd2.LoadSampleDetailsFromRaw") as mocked_load_sample:
+            SANSadd2.add_runs(("LOQ54432", "LOQ54432"), "LOQ", ".raw")
+            self.assertEqual(2, mocked_load_sample.call_count)
+
+    def test_isis_neuxs_files_get_correct_sample_info(self):
+        result = SANSadd2.add_runs(["74014"], "LOQ", ".nxs", rawTypes=(".add", ".raw", ".s*"), lowMem=False)
+        assert result.startswith("The following file has been created:")
+        assert result.endswith("LOQ74014-add.nxs")
+
+        # load the output file and verify it has the sample information
+        ws = Load("LOQ74014-add.nxs")
+        sample = ws.sample()
+        self.assertEqual(3, sample.getGeometryFlag())
+        self.assertEqual(10.0, sample.getHeight())
+        self.assertEqual(10.0, sample.getWidth())
+        self.assertEqual(1.0, sample.getThickness())
+
+    def test_isis_nexus_get_sample_info_using_file_information(self):
+        with patch("SANS.SANSadd2.get_geometry_information_isis_nexus") as mocked_get_geo_info:
+            mocked_get_geo_info.return_value = (8.0, 8.0, 2.0, SampleShape.DISC)
+            SANSadd2.add_runs(("74014", "74014"), "LOQ", ".nxs", rawTypes=(".add", ".raw", ".s*"), lowMem=False)
+            self.assertEqual(1, mocked_get_geo_info.call_count)