Add configuration parameter transmissionErrorTolerance and throw exce…

…ption when the transmission error tolerance is exceeded

scripts/prepare_sensitivities_biosans.py

@@ -48,6 +48,8 @@
 SOLID_ANGLE_CORRECTION = True
 # Flag to do dependent correction with transmission correction
 THETA_DEPENDENT_CORRECTION = True
+# Maximum relative transmission error
+TRANSMISSION_ERROR_TOLERANCE = 0.01
 
 # Single or multiple Flood measurements
 MOVING_DETECTORS = False
@@ -102,6 +104,7 @@
             transmission_flood_runs=TRANSMISSION_FLOOD_RUNS,
             transmission_reference_runs=TRANSMISSION_REFERENCE_RUNS,
             beam_trap_factor=BEAM_TRAP_SIZE_FACTOR,
+            transmission_error_tolerance=TRANSMISSION_ERROR_TOLERANCE,
         )
         preparer.set_theta_dependent_correction_flag(THETA_DEPENDENT_CORRECTION)
 

src/drtsans/configuration/schema/BIOSANS.json

@@ -260,6 +260,10 @@
         },
         "wedge2overlapStitchQmax": {
           "$ref":  "common.json#/definitions/safeStitchQboundsSpecs"
+        },
+        "transmissionErrorTolerance": {
+          "$ref": "common.json#/configuration/transmissionErrorTolerance",
+          "default": 0.01
         }
       },
       "required": ["outputDir", "wavelength", "wavelengthSpread", "useTimeSlice", "timeSliceInterval",

src/drtsans/configuration/schema/EQSANS.json

@@ -312,6 +312,10 @@
           "type": "boolean",
           "default": false,
           "description": "use smallest wavelength as reference wavelength"
+        },
+        "transmissionErrorTolerance": {
+          "$ref": "common.json#/configuration/transmissionErrorTolerance",
+          "default": 0.01
         }
       },
       "required": [

src/drtsans/configuration/schema/GPSANS.json

@@ -106,7 +106,8 @@
         "smearingPixelSizeY": {"$ref":  "common.json#/configuration/smearingPixelSizeY"},
         "useSubpixels":      {"$ref":  "common.json#/configuration/useSubpixels", "default": true},
         "subpixelsX":        {"$ref":  "common.json#/configuration/subpixelsX", "default": 5},
-        "subpixelsY":        {"$ref":  "common.json#/configuration/subpixelsY", "default": 5}
+        "subpixelsY":        {"$ref":  "common.json#/configuration/subpixelsY", "default": 5},
+        "transmissionErrorTolerance": {"$ref": "common.json#/configuration/transmissionErrorTolerance", "default": 0.01}
       },
       "required": ["outputDir", "wavelength", "wavelengthSpread", "useTimeSlice", "timeSliceInterval",
         "timeSliceOffset", "timeSlicePeriod", "useLogSlice", "logSliceName", "logSliceInterval",

src/drtsans/configuration/schema/common.json

@@ -678,6 +678,10 @@
           "wing_detector": ""
         }
       ]
+    },
+    "transmissionErrorTolerance": {
+      "$ref": "common.json#/definitions/safeStringPositiveFloat",
+      "description": "Maximum relative error in the transmission to calculate the transmission correction"
     }
   }
 }

src/drtsans/mono/biosans/api.py

@@ -31,6 +31,7 @@
 from drtsans.stitch import stitch_binned_profiles
 from drtsans.reductionlog import savereductionlog
 from drtsans.thickness_normalization import normalize_by_thickness
+from drtsans.transmission import TransmissionErrorToleranceError
 
 # third party imports
 from mantid.dataobjects import Workspace2D
@@ -1196,6 +1197,7 @@ def reduce_single_configuration(
     sample_trans_value = reduction_input["sample"]["transmission"]["value"]
     bkg_trans_value = reduction_input["background"]["transmission"]["value"]
     theta_dependent_transmission = reduction_config["useThetaDepTransCorrection"]
+    transmission_error_tolerance = reduction_config["transmissionErrorTolerance"]
     mask_panel = None
     if reduction_config["useMaskBackTubes"] is True:
         mask_panel = "back"
@@ -1330,6 +1332,7 @@ def reduce_single_configuration(
             empty_trans_ws,
             radius=transmission_radius,
             radius_unit="mm",
+            transmission_error_tolerance=transmission_error_tolerance,
         )
         logger.notice(f"Background transmission = {bkgd_trans_ws.extractY()[0, 0]}")
 
@@ -1369,6 +1372,7 @@ def _prepare_sample_transmission_ws(_sample_transmission):
             empty_trans_ws,
             radius=transmission_radius,
             radius_unit="mm",
+            transmission_error_tolerance=transmission_error_tolerance,
         )
 
     sample_trans_ws = None
@@ -1488,7 +1492,7 @@ def _prepare_sample_transmission_ws(_sample_transmission):
                         "background": None,
                     },
                 )
-        except ZeroMonitorCountsError as e:
+        except (ZeroMonitorCountsError, TransmissionErrorToleranceError) as e:
             if time_slice:
                 logger.warning(f"Skipping slice {sample_name}: {e}.")
                 continue

src/drtsans/mono/biosans/prepare_sensitivities_correction.py

@@ -180,7 +180,13 @@ def _mask_beam_center(self, flood_ws: MantidWorkspace, beam_center: str) -> Mant
 
         return masked_flood_ws
 
-    def set_transmission_correction(self, transmission_flood_runs, transmission_reference_runs, beam_trap_factor=2):
+    def set_transmission_correction(
+        self,
+        transmission_flood_runs,
+        transmission_reference_runs,
+        beam_trap_factor=2,
+        transmission_error_tolerance=None,
+    ):
         """Set transmission beam run and transmission flood runs
 
         Parameters
@@ -191,6 +197,8 @@ def set_transmission_correction(self, transmission_flood_runs, transmission_refe
             transmission reference runs
         beam_trap_factor : float, int
             factor to beam trap size for masking angle
+        transmission_error_tolerance: float
+            Maximum relative transmission error
 
         Returns
         -------
@@ -228,6 +236,8 @@ def format_run_or_runs(run_s):
         # Set the beam trap factor for transmission reference and flood run to mask angle
         self._biosans_beam_trap_factor = beam_trap_factor
 
+        self._transmission_error_tolerance = transmission_error_tolerance
+
     def set_theta_dependent_correction_flag(self, flag):
         """Set the flag to do theta dep with transmission correction
 
@@ -320,7 +330,11 @@ def _apply_transmission_correction(self, flood_ws, transmission_beam_run, transm
         )
 
         # Zero-Angle Transmission Co-efficients
-        transmission_corr_ws = calculate_transmission(transmission_flood_ws, transmission_workspace)
+        transmission_corr_ws = calculate_transmission(
+            transmission_flood_ws,
+            transmission_workspace,
+            transmission_error_tolerance=self._transmission_error_tolerance,
+        )
         average_zero_angle = np.mean(transmission_corr_ws.readY(0))
         average_zero_angle_error = np.linalg.norm(transmission_corr_ws.readE(0))
         logger.notice(

src/drtsans/mono/gpsans/api.py

@@ -1110,6 +1110,7 @@ def reduce_single_configuration(loaded_ws, reduction_input, prefix="", skip_nan=
     sample_trans_value = reduction_input["sample"]["transmission"]["value"]
     bkg_trans_value = reduction_input["background"]["transmission"]["value"]
     theta_deppendent_transmission = reduction_config["useThetaDepTransCorrection"]
+    transmission_error_tolerance = reduction_config["transmissionErrorTolerance"]
     mask_panel = None
     if reduction_config["useMaskBackTubes"]:
         mask_panel = "back"
@@ -1218,6 +1219,7 @@ def reduce_single_configuration(loaded_ws, reduction_input, prefix="", skip_nan=
             empty_trans_ws,
             radius=transmission_radius,
             radius_unit="mm",
+            transmission_error_tolerance=transmission_error_tolerance,
         )
         logger.notice(f"Background transmission = {bkgd_trans_ws.extractY()[0, 0]}")
         background_transmission_dict = {
@@ -1246,6 +1248,7 @@ def reduce_single_configuration(loaded_ws, reduction_input, prefix="", skip_nan=
             empty_trans_ws,
             radius=transmission_radius,
             radius_unit="mm",
+            transmission_error_tolerance=transmission_error_tolerance,
         )
         logger.notice(f"Sample transmission = {sample_trans_ws.extractY()[0, 0]}")
         sample_transmission_dict = {

src/drtsans/mono/transmission.py

@@ -7,7 +7,45 @@
 __all__ = ["calculate_transmission", "apply_transmission_correction"]
 
 
-def calculate_transmission(input_sample, input_reference, radius=None, radius_unit="mm", output_workspace=None):
+def calculate_transmission(
+    input_sample,
+    input_reference,
+    radius=None,
+    radius_unit="mm",
+    transmission_error_tolerance=None,
+    output_workspace=None,
+):
+    """
+    Calculate the raw transmission coefficients at zero scattering angle
+    from already prepared sample and reference data.
+
+    Parameters
+    ----------
+    input_sample: str, ~mantid.api.MatrixWorkspace, ~mantid.api.IEventWorkspace
+        Prepared sample workspace (possibly obtained with an attenuated beam)
+    input_reference: str, ~mantid.api.MatrixWorkspace, ~mantid.api.IEventWorkspace
+        Prepared direct beam workspace (possibly obtained with an attenuated beam)
+    radius: float
+        Radius around the beam center for pixel integration, in millimeters.
+        If None, radius will be obtained or calculated using `input_reference` workspace.
+    radius_unit: str
+        Either 'mm' or 'm', and only used in conjunction with option `radius`.
+    transmission_error_tolerance: float
+        Maximum relative error for transmission
+    output_workspace: str
+        Name of the output workspace containing the raw transmission values.
+        If None, a hidden random name will be provided.
+
+    Returns
+    -------
+    ~mantid.api.MatrixWorkspace
+        Workspace containing the raw transmission values
+
+    Raises
+    ------
+    TransmissionToleranceError
+        If there is insufficient statistics to calculate the transmission correction
+    """
     if radius is None:
         logger.information("Calculating beam radius from sample logs")
         radius = beam_radius(input_reference, unit="mm")
@@ -17,6 +55,7 @@ def calculate_transmission(input_sample, input_reference, radius=None, radius_un
         input_reference,
         radius,
         radius_unit=radius_unit,
+        transmission_error_tolerance=transmission_error_tolerance,
         output_workspace=output_workspace,
     )
 

src/drtsans/tof/eqsans/api.py

@@ -696,6 +696,7 @@ def reduce_single_configuration(
     sample_trans_value = reduction_input["sample"]["transmission"]["value"]
     bkg_trans_value = reduction_input["background"]["transmission"]["value"]
     theta_dependent_transmission = reduction_config["useThetaDepTransCorrection"]
+    transmission_error_tolerance = reduction_config["transmissionErrorTolerance"]
     mask_panel = "back" if reduction_config["useMaskBackTubes"] is True else None
     output_suffix = ""
 
@@ -769,6 +770,7 @@ def reduce_single_configuration(
         "sample",
         output_dir,
         outputFilename,
+        transmission_error_tolerance,
     )
     (sample_trans_ws, sample_transmission_dict, sample_transmission_raw_dict) = sample_returned
 
@@ -792,6 +794,7 @@ def reduce_single_configuration(
             "bkgd",
             output_dir,
             base_out_name,
+            transmission_error_tolerance,
         )
     else:
         bkgd_returned = (None, None, None)
@@ -826,6 +829,7 @@ def reduce_single_configuration(
                 "elasticref",
                 None,
                 None,
+                transmission_error_tolerance,
             )
         else:
             output = (None, None, None)
@@ -846,6 +850,7 @@ def reduce_single_configuration(
                 "elasticrefbkgd",
                 None,
                 None,
+                transmission_error_tolerance,
             )
         else:
             output = (None, None, None)

src/drtsans/tof/eqsans/reduction_api.py

@@ -144,7 +144,46 @@ def process_transmission(
     type_name,
     output_dir,
     output_file_name,
+    transmission_error_tolerance=None,
 ):
+    """
+    Prepares workspaces and calculates transmission
+
+    Parameters
+    ----------
+    transmission_ws
+        Sample transmission workspace
+    empty_trans_ws
+        Empty beam transmission workspace
+    transmission_radius
+        Radius around the beam center for pixel integration, in millimeters.
+        If None, radius will be obtained or calculated using `input_reference` workspace.
+    transmission_error_tolerance: float
+        Maximum relative error for transmission
+    sensitivity_ws
+        Sensitivity workspace
+    flux_method: str
+        Method for flux normalization. Either 'monitor', or 'time'.
+    flux: str
+        if ``flux_method`` is proton charge, then path to file containing the
+        wavelength distribution of the neutron flux. If ``flux method`` is
+        monitor, then path to file containing the flux-to-monitor ratios.
+        if ``flux_method`` is time, then pass one log entry name such
+        as ``duration`` or leave it as :py:obj:`None` for automatic log search.
+    prefix: str
+        Prefix for transmission workspace name
+    type_name: str
+        String used in transmission workspace name to denote type (e.g. sample/background)
+    output_dir: str
+        Output directory for transmission output
+    output_file_name: str
+        Output filename prefix for transmission output
+
+    Returns
+    -------
+    (~mantid.api.MatrixWorkspace, dict, dict)
+        transmission workspace, processed transmission dictionary, raw transmission dictionary
+    """
     # sample transmission
     processed_transmission_dict = {}  # for output log
     raw_transmission_dict = {}  # for output log
@@ -166,6 +205,7 @@ def process_transmission(
             empty_trans_ws,
             radius=transmission_radius,
             radius_unit="mm",
+            transmission_error_tolerance=transmission_error_tolerance,
         )
         print(f"{type_name} transmission =", calculated_trans_ws.extractY()[0, 0])
 
@@ -186,6 +226,7 @@ def process_transmission(
                 radius=transmission_radius,
                 radius_unit="mm",
                 fit_function="",
+                transmission_error_tolerance=transmission_error_tolerance,
             )
 
             raw_tr_fn = os.path.join(output_dir, f"{output_file_name}_raw_trans.txt")

src/drtsans/tof/eqsans/transmission.py

@@ -32,6 +32,7 @@ def calculate_transmission(
     input_reference,
     radius=None,
     radius_unit="mm",
+    transmission_error_tolerance=None,
     fit_function="name=LinearBackground",
     output_workspace=None,
     output_raw_transmission=None,
@@ -54,6 +55,8 @@ def calculate_transmission(
         If None, radius will be obtained or calculated using ``input_reference``.
     radius_unit: str
         Either 'mm' or 'm', and only used in conjunction with option ``radius``.
+    transmission_error_tolerance: float
+        Maximum relative error for transmission
     fit_function: str
         String representation of the fit function. See Mantid's
         :ref:`UserFunction <func-UserFunction>` or any of Mantid's built-in functions.
@@ -90,6 +93,7 @@ def calculate_transmission(
         input_reference,
         radius=radius,
         radius_unit=radius_unit,
+        transmission_error_tolerance=transmission_error_tolerance,
         output_workspace=output_raw_transmission,
     )
     if bool(fit_function) is True: