Fix errors in handling pause, and MD workspaces with no UB (#142)

* Fix errors in handling pause, and MD workspaces with no UB

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Update sample.py

* Update sample.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* docstring

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/shiver/models/convert_dgs_to_single_mde.py

@@ -296,7 +296,9 @@ def PyExec(self):  # pylint: disable=too-many-branches
 
         # do filtering
         if units == "TOF" and len(CheckForSampleLogs(Workspace=data, LogNames="pause")) == 0:
-            data = FilterByLogValue(InputWorkspace=data, LogName="pause", MinimumValue=-1, MaximumValue=0.5)
+            data = FilterByLogValue(
+                InputWorkspace=data, LogName="pause", MinimumValue=-1, MaximumValue=0.5, LogBoundary="Left"
+            )
         if units == "TOF" and bad_pulses_threshold > 0:
             data = FilterBadPulses(InputWorkspace=data, LowerCutoff=bad_pulses_threshold)
 

src/shiver/models/sample.py

@@ -38,11 +38,17 @@ def connect_error_message(self, callback):
     def get_lattice_ub(self):
         """return oriented lattice object from mtd - if no name provided initialize lattice"""
         if self.name:
-            if mtd.doesExist(self.name):
-                self.oriented_lattice = mtd[self.name].getExperimentInfo(0).sample().getOrientedLattice()
-                return self.oriented_lattice
-            err_msg = f"Workspace {self.name} does not exist. Lattice from default parameters\n"
-            logger.error(err_msg)
+            try:
+                if mtd.doesExist(self.name):
+                    self.oriented_lattice = mtd[self.name].getExperimentInfo(0).sample().getOrientedLattice()
+                    return self.oriented_lattice
+                err_msg = f"Workspace {self.name} does not exist. Lattice from default parameters\n"
+                logger.error(err_msg)
+            except RuntimeError:
+                err_msg = (
+                    f"Workspace {self.name} does not contain an OrientedLattice. Lattice from default parameters\n"
+                )
+                logger.error(err_msg)
         # no valid name-workspace provided, create lattice with initial params
         params = {
             "a": 1.00000,

tests/models/test_generatemde.py

@@ -23,6 +23,7 @@
     LoadNexusMonitors,
     GetEiT0atSNS,
     DgsReduction,
+    AddTimeSeriesLog,
     CropWorkspace,
     ConvertToMD,
     ConvertToMDMinMaxGlobal,
@@ -60,6 +61,16 @@ def test_convert_dgs_to_single_mde_single_qsample():
     assert CompareMDWorkspaces(md1, md2, IgnoreBoxID=True)[0]
 
 
+def test_convert_dgs_to_single_pause():
+    """Test for correctly handling pause"""
+    raw_data_folder = os.path.join(os.path.dirname(__file__), "../data/raw")
+
+    data = LoadEventNexus(os.path.join(raw_data_folder, "HYS_178921.nxs.h5"))
+    AddTimeSeriesLog(Workspace=data, Name="pause", Time="2017-11-02T01:48:58.543570666", Value=1, Type="int")
+    md_p = ConvertDGSToSingleMDE(InputWorkspace=data, Ei=25.0, T0=112.0, TimeIndependentBackground="Default")
+    assert md_p.getNEvents() == 6140  # the original mde has 23682 events
+
+
 def test_convert_dgs_to_single_mde_single_qlab():
     """Test for QFrame=Q_lab option ConvertDGSToSingleMDE"""
 

tests/models/test_sample_parameters_buttons_actions.py

@@ -4,8 +4,23 @@
 import numpy as np
 from pytest import approx
 
+from mantid.kernel import amend_config
+
 # pylint: disable=no-name-in-module
-from mantid.simpleapi import LoadMD, mtd
+from mantid.simpleapi import (
+    LoadMD,
+    LoadEventNexus,
+    mtd,
+    ConvertToMD,
+    SetGoniometer,
+    MaskBTP,
+    FilterByLogValue,
+    LoadNexusMonitors,
+    GetEiT0atSNS,
+    DgsReduction,
+    CropWorkspace,
+    ConvertToMDMinMaxGlobal,
+)
 from shiver.models.sample import SampleModel
 from shiver.models.generate import gather_mde_config_dict
 
@@ -119,6 +134,93 @@ def error_callback(msg):
     assert v_array == approx(param_v_array)
 
 
+def test_apply_button_valid_mde_ub():
+    """Test for pressing Apply button with mde workspace that does not have ub"""
+
+    name = "out_data"
+
+    datafile = os.path.join(os.path.dirname(__file__), "../data/raw", "SEQ_124735.nxs.h5")
+
+    # Manual data reduction
+    LoadEventNexus(Filename=datafile, OutputWorkspace="data")
+    SetGoniometer(Workspace="data", Axis0="phi,0,1,0,1")
+    MaskBTP(Workspace="data", Pixel="1-7,122-128")
+    MaskBTP(Workspace="data", Bank="114,115,75,76,38,39")
+    MaskBTP(Workspace="data", Bank="88", Tube="2-4", Pixel="30-35")
+    MaskBTP(Workspace="data", Bank="127", Tube="7-8", Pixel="99-128")
+    MaskBTP(Workspace="data", Bank="99-102")
+    MaskBTP(Workspace="data", Bank="38-42", Pixel="120-128")
+    MaskBTP(Workspace="data", Bank="43", Pixel="119-128")
+    MaskBTP(Workspace="data", Bank="44-48", Pixel="120-128")
+    MaskBTP(Workspace="data", Bank="74", Tube="8")
+    MaskBTP(Workspace="data", Bank="96", Tube="8")
+    MaskBTP(Workspace="data", Bank="130-132", Pixel="113-128")
+    MaskBTP(Workspace="data", Bank="148", Tube="4")
+    MaskBTP(Workspace="data", Bank="46", Tube="6-8", Pixel="105-110")
+
+    FilterByLogValue(InputWorkspace="data", LogName="pause", MinimumValue=-1, MaximumValue=0.5, OutputWorkspace="data")
+
+    LoadNexusMonitors(Filename=datafile, OutputWorkspace="__MonWS")
+    e_i, t_0 = GetEiT0atSNS(MonitorWorkspace="__MonWS", IncidentEnergyGuess="35")
+    with amend_config(facility="SNS"):
+        DgsReduction(
+            SampleInputWorkspace="data",
+            SampleInputMonitorWorkspace="__MonWS",
+            IncidentEnergyGuess=e_i,
+            UseIncidentEnergyGuess=True,
+            TimeZeroGuess=t_0,
+            EnergyTransferRange="-17.5,1,31.5",
+            SofPhiEIsDistribution=False,
+            OutputWorkspace="dgs",
+        )
+    CropWorkspace(InputWorkspace="dgs", OutputWorkspace="dgs", XMin="-17.5", XMax="31.5")
+    min_values, max_values = ConvertToMDMinMaxGlobal(
+        InputWorkspace="dgs", QDimensions="Q3D", dEAnalysisMode="Direct", Q3DFrames="Q"
+    )
+
+    ConvertToMD(
+        InputWorkspace="dgs",
+        QDimensions="Q3D",
+        dEAnalysisMode="Direct",
+        Q3DFrames="Q_sample",
+        MinValues=min_values,
+        MaxValues=max_values,
+        MaxRecursionDepth=2,
+        OutputWorkspace=name,
+    )
+
+    # workspace does not have a ub
+    sample_model = SampleModel(name)
+
+    errors = []
+    params = {}
+
+    params["a"] = 4.44000
+    params["b"] = 4.44000
+    params["c"] = 4.44000
+    params["alpha"] = 90.0
+    params["beta"] = 90.0
+    params["gamma"] = 90.0
+    params["u"] = "0.00,-0.00,4.40"
+    params["v"] = "4.12717,4.12717,-0.000"
+
+    def error_callback(msg):
+        errors.append(msg)
+
+    sample_model.connect_error_message(error_callback)
+    sample_model.set_ub(params)
+
+    # check if the oriented lattice is updated
+    assert len(errors) == 0
+
+    assert sample_model.oriented_lattice.a() == params["a"]
+    assert sample_model.oriented_lattice.a() == params["b"]
+    assert sample_model.oriented_lattice.b() == params["c"]
+    assert sample_model.oriented_lattice.alpha() == approx(params["alpha"])
+    assert sample_model.oriented_lattice.beta() == approx(params["beta"])
+    assert sample_model.oriented_lattice.gamma() == approx(params["gamma"])
+
+
 def test_apply_button_invalid():
     """Test for pressing Apply button with invalid input"""