Merge pull request #998 from neutrons/expunge_correct_tof_offset

remove correct_tof_offset

docs/release_notes.rst

@@ -23,6 +23,7 @@ Release Notes
 
 **Of interest to the User**:
 
+- PR #998: remove the TOF offset that is done by the data aquisition system
 - PR #994: Remove unused module `drtsans/tof/eqsans/reduce.py`
 - PR #993: Skip slices with too high transmission error when using time sliced sample transmission run
 - PR #325: Migrates repository from GitLab to GitHub

src/drtsans/tof/eqsans/correct_frame.py

@@ -17,7 +17,6 @@
     logger,
     SetInstrumentParameter,
     ModeratorTzero,
-    ChangeBinOffset,
 )
 from drtsans.samplelogs import SampleLogs
 from drtsans.tof.eqsans.chopper import EQSANSDiskChopperSet
@@ -418,25 +417,6 @@ def correct_emission_time(input_workspace):
     )
 
 
-def correct_tof_offset(input_workspace):
-    r"""
-    This corrects the TOF offset when running in 60Hz, non-frameskip. A
-    constant 664.7us needs to be removed, otherwise nothing is changed.
-
-    Parameters
-    ----------
-    input_workspace: ~mantid.api.IEventsWorkspace
-        Data workspace
-    """
-    # If 60Hz (non-frameskip) then subtract 664.7us from all tofs
-    if not _is_frame_skipping(input_workspace):
-        ChangeBinOffset(
-            InputWorkspace=input_workspace,
-            OutputWorkspace=input_workspace,
-            Offset=-664.7,
-        )
-
-
 def smash_monitor_spikes(input_workspace, output_workspace=None):
     r"""
     Detect and remove spikes in monitor data TOF between min and max TOF's.

src/drtsans/tof/eqsans/load.py

@@ -22,7 +22,6 @@
     transform_to_wavelength,
     smash_monitor_spikes,
     set_init_uncertainties,
-    correct_tof_offset,
     correct_emission_time,
 )
 from drtsans.tof.eqsans.geometry import source_monitor_distance
@@ -180,8 +179,6 @@ def load_events(
     # EQSANS specific part benefits from converting workspace to a string
     output_workspace = str(output_workspace)
 
-    # Correct TOF offset
-    correct_tof_offset(output_workspace)
     # Correct TOF of detector
     correct_detector_frame(output_workspace, path_to_pixel=path_to_pixel)
     # Correct TOF for emission time
@@ -504,8 +501,6 @@ def load_and_split(
     )
 
     for _w in ws_group:
-        # Correct TOF offset
-        correct_tof_offset(_w)
         # Correct TOF of detector
         correct_detector_frame(_w, path_to_pixel=path_to_pixel)
         # Correct TOF for emission time

tests/integration/drtsans/tof/eqsans/test_elastic_and_inelastic_corrections.py

@@ -377,12 +377,14 @@ def _run_reduction_and_compare(config, expected_result_basename):
         test_iq1d_file = os.path.join(test_dir, config["outputFileName"] + "_Iq.dat")
         gold_iq1d_file = os.path.join(datarepo_dir.eqsans, "test_corrections", expected_result_basename + "_Iq.dat")
         # compare
-        np.testing.assert_allclose(np.loadtxt(test_iq1d_file), np.loadtxt(gold_iq1d_file))
+        np.testing.assert_allclose(np.loadtxt(test_iq1d_file), np.loadtxt(gold_iq1d_file), atol=0.003)
 
         test_iq2d_file = os.path.join(test_dir, config["outputFileName"] + "_Iqxqy.dat")
         gold_iq2d_file = os.path.join(datarepo_dir.eqsans, "test_corrections", expected_result_basename + "_Iqxqy.dat")
         # compare
-        np.testing.assert_allclose(np.loadtxt(test_iq2d_file, skiprows=4), np.loadtxt(gold_iq2d_file, skiprows=4))
+        np.testing.assert_allclose(
+            np.loadtxt(test_iq2d_file, skiprows=4), np.loadtxt(gold_iq2d_file, skiprows=4), atol=0.003
+        )
 
         DeleteWorkspace("_empty")
         DeleteWorkspace("_mask")

tests/integration/drtsans/tof/eqsans/test_integration_api.py

@@ -41,9 +41,9 @@
     ("EQSANS_86217", 508339, 1300, 14122, 9595, 59633, True, 2.61, 14.72, 540),
     ("EQSANS_92353", 262291, 4000, 14122, 11288, 61309, True, 2.59, 12.98, 431),
     ("EQSANS_85550", 270022, 5000, 14122, 11914, 61930, True, 2.59, 12.43, 599),
-    ("EQSANS_101595", 289989, 1300, 14122, 7649, 24392, False, 2.11, 5.65, 141),
-    ("EQSANS_88565", 19362, 4000, 14122, 45485, 62174, False, 10.02, 13.2, 694),
-    ("EQSANS_88901", 340431, 8000, 14122, 66629, 83378, False, 11.99, 14.62, 54377),
+    ("EQSANS_101595", 289989, 1300, 14122, 7657, 24384, False, 2.11, 5.65, 150),
+    ("EQSANS_88565", 19362, 4000, 14122, 45486, 62172, False, 10.02, 13.2, 743),
+    ("EQSANS_88901", 340431, 8000, 14122, 67202, 83868, False, 11.99, 14.62, 56013),
 )
 
 run_sets = [{k: v for k, v in zip(keys, value)} for value in values]

tests/unit/drtsans/tof/eqsans/test_api.py

@@ -59,18 +59,16 @@ def test_load_all_files_simple_interval(datarepo_dir):
     assert len(loaded.sample) == 1
     history = loaded.sample[0].data.getHistory()
 
-    assert history.size() == 11
+    assert history.size() == 10
     assert history.getAlgorithm(0).name() == "LoadEventNexus"
     assert history.getAlgorithm(0).getProperty("Filename").value.endswith("sns/eqsans/EQSANS_105428.nxs.h5")
     assert history.getAlgorithm(2).name() == "MoveInstrumentComponent"
-    assert history.getAlgorithm(3).name() == "ChangeBinOffset"
-    assert history.getAlgorithm(4).name() == "SetInstrumentParameter"
-    # assert history.getAlgorithm(4).name() == "ModeratorTZero"
-    assert history.getAlgorithm(6).name() == "MoveInstrumentComponent"
-    assert history.getAlgorithm(7).name() == "ConvertUnits"
-    assert history.getAlgorithm(8).name() == "Rebin"
-    assert history.getAlgorithm(9).name() == "SetUncertainties"
-    assert history.getAlgorithm(10).name() == "AddSampleLogMultiple"
+    assert history.getAlgorithm(3).name() == "SetInstrumentParameter"
+    assert history.getAlgorithm(5).name() == "MoveInstrumentComponent"
+    assert history.getAlgorithm(6).name() == "ConvertUnits"
+    assert history.getAlgorithm(7).name() == "Rebin"
+    assert history.getAlgorithm(8).name() == "SetUncertainties"
+    assert history.getAlgorithm(9).name() == "AddSampleLogMultiple"
 
     assert loaded.background.data is None
     assert loaded.background_transmission.data is None
@@ -86,7 +84,7 @@ def test_load_all_files_simple_interval(datarepo_dir):
 
     # check interval
     w = loaded.sample[0].data
-    assert int(w.extractY().sum()) == 706
+    assert int(w.extractY().sum()) == 773
 
     # Change reduction input and rerun load_all_files
     reduction_input["configuration"]["useDefaultMask"] = True
@@ -132,18 +130,16 @@ def test_load_all_files_simple(datarepo_dir):
     assert len(loaded.sample) == 1
     history = loaded.sample[0].data.getHistory()
 
-    assert history.size() == 11
+    assert history.size() == 10
     assert history.getAlgorithm(0).name() == "LoadEventNexus"
     assert history.getAlgorithm(0).getProperty("Filename").value.endswith("sns/eqsans/EQSANS_105428.nxs.h5")
     assert history.getAlgorithm(2).name() == "MoveInstrumentComponent"
-    assert history.getAlgorithm(3).name() == "ChangeBinOffset"
-    assert history.getAlgorithm(4).name() == "SetInstrumentParameter"
-    # assert history.getAlgorithm(4).name() == "ModeratorTZero"
-    assert history.getAlgorithm(6).name() == "MoveInstrumentComponent"
-    assert history.getAlgorithm(7).name() == "ConvertUnits"
-    assert history.getAlgorithm(8).name() == "Rebin"
-    assert history.getAlgorithm(9).name() == "SetUncertainties"
-    assert history.getAlgorithm(10).name() == "AddSampleLogMultiple"
+    assert history.getAlgorithm(3).name() == "SetInstrumentParameter"
+    assert history.getAlgorithm(5).name() == "MoveInstrumentComponent"
+    assert history.getAlgorithm(6).name() == "ConvertUnits"
+    assert history.getAlgorithm(7).name() == "Rebin"
+    assert history.getAlgorithm(8).name() == "SetUncertainties"
+    assert history.getAlgorithm(9).name() == "AddSampleLogMultiple"
 
     assert loaded.background.data is None
     assert loaded.background_transmission.data is None

tests/unit/drtsans/tof/eqsans/test_correct_frame.py

@@ -338,27 +338,5 @@ def test_correct_emission_time_30Hz(clean_workspace):
     assert_allclose(w.getSpectrum(0).getTofs() * 10000 * h / (z * m), expected_wl, rtol=1e-4)
 
 
-def test_correct_tof_offset(clean_workspace):
-    # Make a simple workspace with correct distances and add tofs to it
-    w = CreateSampleWorkspace("Event", NumBanks=1, BankPixelWidth=1, NumEvents=10)
-    clean_workspace(w)
-
-    starting_tofs = w.getSpectrum(0).getTofs()
-
-    # set the workspace to frame_skipping, the tofs should be unchanged
-    SampleLogs(w).insert("is_frame_skipping", 1)
-    # run correct_tof_offset on workspace
-    correct_frame.correct_tof_offset(w)
-    # compare starting and final tofs
-    assert_allclose(w.getSpectrum(0).getTofs(), starting_tofs)
-
-    # set the workspace to not frame_skipping, the tofs should be changed by 664.7
-    SampleLogs(w).insert("is_frame_skipping", 0)
-    # run correct_tof_offset on workspace
-    correct_frame.correct_tof_offset(w)
-    # compare starting and final tofs with expected difference
-    assert_allclose(w.getSpectrum(0).getTofs(), starting_tofs - 664.7)
-
-
 if __name__ == "__main__":
     pytest.main([__file__])

tests/unit/drtsans/tof/eqsans/test_load.py

@@ -96,10 +96,10 @@ def test_merge_Data(datarepo_dir):
     assert merged_sample_logs.proton_charge.size() == 12933 + 17343 + 4341
 
     # Check integrated intensity increases as the total sum
-    assert mtd[str(ws0)].extractY().sum() == 284923
-    assert mtd[str(ws1)].extractY().sum() == 1368485
+    assert mtd[str(ws0)].extractY().sum() == 288830
+    assert mtd[str(ws1)].extractY().sum() == 1338500
     assert mtd[str(ws2)].extractY().sum() == 65694
-    assert mtd[str(merged_workspaces)].extractY().sum() == 284923 + 1368485 + 65694
+    assert mtd[str(merged_workspaces)].extractY().sum() == 288830 + 1338500 + 65694
 
     mtd.remove(str(ws0))
     mtd.remove(str(ws1))
@@ -233,11 +233,11 @@ def test_load_and_split_and_histogram(datarepo_dir, clean_workspace):
 
     # check values for Y and E don't change unexpectedly
     assert filtered_ws.getItem(0).extractY().max() == 4
-    assert filtered_ws.getItem(1).extractY().max() == 25
+    assert filtered_ws.getItem(1).extractY().max() == 27
     assert filtered_ws.getItem(2).extractY().max() == 3
     assert filtered_ws.getItem(0).extractE().max() == pytest.approx(2, abs=1e-7)
-    assert filtered_ws.getItem(1).extractE().max() == pytest.approx(5, abs=1e-7)
-    assert filtered_ws.getItem(2).extractE().max() == pytest.approx(1.7320508, abs=1e-7)
+    assert filtered_ws.getItem(1).extractE().max() == pytest.approx(5.2, abs=0.1)
+    assert filtered_ws.getItem(2).extractE().max() == pytest.approx(1.7, abs=0.1)
 
     # check metadata is set correctly
     assert SampleLogs(filtered_ws.getItem(0)).slice.value == 1

tests/unit/drtsans/tof/eqsans/test_normalization.py

@@ -207,7 +207,7 @@ def test_normalize_by_monitor(flux_to_monitor, data_ws, monitor_ws, temp_workspa
     data_workspace_normalized = SumSpectra(data_workspace_normalized, OutputWorkspace=data_workspace_normalized.name())
     # Second we integrate over all wavelength bins and check the value  will not change as the code in the
     # repository evolves
-    assert sum(data_workspace_normalized.dataY(0)) == approx(0.621, abs=1e-03)
+    assert sum(data_workspace_normalized.dataY(0)) == approx(0.552, abs=1e-03)
 
 
 @pytest.mark.datarepo
@@ -315,7 +315,7 @@ def test_normalize_by_flux(beam_flux, flux_to_monitor, data_ws, monitor_ws, temp
     # then we integrate this single spectrum over all wavelengths
     total_normalized_intensity = sum(summed_normalized.readY(0))
     # here we just check that the result will not change as the code in the repository evolves
-    assert total_normalized_intensity == approx(0.621, abs=1e-3)
+    assert total_normalized_intensity == approx(0.552, abs=1e-3)
 
     #
     # Third we normalize by run duration with method='time'